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<p>Dima Golovenko: Removing all content from page</p> <hr /> <div></div>

Dima Golovenko https://proteopedia.org/index.php?title=User:Dima_Golovenko/R.EcoRII&diff=1094230 User:Dima Golovenko/R.EcoRII 2010-06-11T15:44:12Z

<p>Dima Golovenko: /* Effector-binding domain */</p> <hr /> <div><br /> {{STRUCTURE_1na6| PDB=1na6 | SCENE= }} <br /> <br /> ===Crystal structure of restriction endonuclease EcoRII mutant R88A===<br /> <br /> <br /> {{ABSTRACT_PUBMED_14659759}}<br /> <br /> ==About this Structure==<br /> 1NA6 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NA6 OCA]. <br /> <br /> [[Restriction endonuclease]] (REase) '''EcoRII''' (pronounced "eco R two") is an [[enzyme]] of [[restriction modification system]] (RM) naturally found in ''[[Escherichia coli]]'', a [[Gram-negative bacteria]]. Its [[molecular mass]] is 45.2 [[Atomic mass unit|kDa]], being composed of 402 [[amino acids]].<ref name="title">{{cite web | url = http://rebase.neb.com/rebase/enz/EcoRII.html | title = EcoRII | accessdate = 2008-03-23 | author = Richard J. Roberts | authorlink = | coauthors = | date = | format = | work = REBASE - The Restriction Enzyme Database | publisher = | pages = | language = | archiveurl = | archivedate = | quote = }}</ref><br /> <br /> ==Mode of action==<br /> EcoRII is a [[bacterial]] Type IIE<ref name="pmid12654995">{{cite journal | author = Roberts RJ, Belfort M, Bestor T, ''et al.'' | title = A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes | journal = Nucleic Acids Res. | volume = 31 | issue = 7 | pages = 1805–12 | year = 2003 | pmid = 12654995 | doi = 10.1093/nar/gkg274 | pmc = 152790 }} [http://nar.oxfordjournals.org/cgi/reprint/31/7/1805.pdf PDF] </ref> [[restriction endonuclease|REase]] that interacts with two<ref name="pmid10903314">{{cite journal | author = Mücke M, Lurz R, Mackeldanz P, Behlke J, Krüger DH, Reuter M | title = Imaging DNA loops induced by restriction endonuclease EcoRII. A single amino acid substitution uncouples target recognition from cooperative DNA interaction and cleavage | journal = J. Biol. Chem. | volume = 275 | issue = 39 | pages = 30631–7 | year = 2000 | pmid = 10903314 | doi = 10.1074/jbc.M003904200 }}[http://www.jbc.org/cgi/reprint/275/39/30631.pdf PDF]</ref> or [http://pubs.acs.org/isubscribe/journals/bichaw/46/i39/figures/bi701123un00001.gif three]<ref name="pmid17845057">{{cite journal | author = Shlyakhtenko LS, Gilmore J, Portillo A, Tamulaitis G, Siksnys V, Lyubchenko YL | title = Direct visualization of the EcoRII-DNA triple synaptic complex by atomic force microscopy | journal = Biochemistry | volume = 46 | issue = 39 | pages = 11128–36 | year = 2007 | pmid = 17845057 | doi = 10.1021/bi701123u }}</ref> copies of the pseudopalindromic [[dsDNA|DNA]] [[Restriction_enzyme#Recognition_site|recognition sequence]] [[5' end|5']]-[[Cytosine|CC]]W[[Guanine|GG]]-[[3' end|3']] ([[W]] = [[Adenine|A]] or [[Thymine|T]]), one being the actual target of cleavage, the other(s) serving as the [[Allosteric regulation#Allosteric activation and inhibition|allosteric activator]](s). EcoRII cut target [[dsDNA|DNA]] sequence CCWGG generating [[sticky ends]].<ref name="isbn0-7167-3520-2">{{cite book | author = Griffiths, Anthony J. F. | title = An Introduction to genetic analysis | publisher = W.H. Freeman | location = San Francisco | year = 1999 | pages = | isbn = 0-7167-3520-2 | oclc = | doi = }}</ref><br /> <br /> ==Cut diagram==<br /> {| class="wikitable"<br /> | Recognition site<br /> | Cut results<br /> |- <br /> | <br /> 5' NN'''CCWGG'''NN<br /> 3' NN'''GGWCC'''NN <br /> |<br /> 5' NN '''CCWGG'''NN<br /> 3' NN'''GGWCC''' NN<br /> |}<br /> <br /> ==Structure==<br /> The [[apo]] [[X-ray crystallography|crystal]] [[protein structure|structure]] of EcoRII [[Point mutation|mutant]] R88A ({{PDB|1NA6}})<ref name="Zhou_2004">{{cite journal | author = Zhou XE, Wang Y, Reuter M, Mücke M, Krüger DH, Meehan EJ, Chen L | title = Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold | journal = J. Mol. Biol. | volume = 335 | issue = 1 | pages = 307–19 | year = 2004 | pmid = 14659759 | doi = 10.1016/j.jmb.2003.10.030 }}</ref> has been solved at 2.1 [[Å]] [[Resolution (electron density)|resolution]]. The EcoRII [[Primary structure|monomer]] has two [[Protein domains|domains]], [[N-terminus|N-terminal]] and [[C-terminus|C-terminal]], linked through a [[hinge]] [[turn (biochemistry)|loop]]. <br /> <br /> ===Effector-binding domain===<br /> * <scene name='User:Dima_Golovenko/R.EcoRII/Effector_domain/1'>The N-terminal</scene> [[Effector (biology)|effector]]-[[DNA-binding domain|binding domain]] has a archetypal DNA-binding pseudobarrel fold ({{SCOP|101936}}) with a prominent [[structural motif|cleft]]. [[Structural alignment#DALI|Structural superposition]] showed it is evolutionarily related to:<br /> *[[B3 DNA binding domain]] ({{SCOP|117343}}) from the [[transcription factors]] in [[higher plants]] ({{PDB|1WID}})<ref name="pmid15548737">{{cite journal | author = Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Tomo Y, Hayami N, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S | title = Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1 | journal = Plant Cell | volume = 16 | issue = 12 | pages = 3448–59 | year = 2004 | pmid = 15548737 | doi = 10.1105/tpc.104.026112 | pmc = 535885 }}[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=535885&blobtype=pdf PDF]</ref><br /> *C-terminal domain of [[restriction endonuclease]] BfiI<ref name="BfiI">{{cite web | url = http://rebase.neb.com/rebase/enz/BfiI.html | title = BfiI | accessdate = 2008-03-23 | author = Richard J. Roberts | authorlink = | coauthors = | date = | format = | work = REBASE - The Restriction Enzyme Database | publisher = | pages = | language = | archiveurl = | archivedate = | quote = }}</ref> ({{PDB|2C1L}})<ref name="pmid16247004">{{cite journal | author = Grazulis S, Manakova E, Roessle M, Bochtler M, Tamulaitiene G, Huber R, Siksnys V | title = Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease | journal = Proc. Natl. Acad. Sci. U.S.A. | volume = 102 | issue = 44 | pages = 15797–802 | year = 2005 | pmid = 16247004 | doi = 10.1073/pnas.0507949102 | pmc = 1266039 }} [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1266039&blobtype=pdf PDF]</ref><br /> <br /> ===Catalytic domain===<br /> <scene name='User:Dima_Golovenko/R.EcoRII/Catalytic_domain/1'>The catalytic domain</scene> has a typical<ref name="pmid17369272">{{cite journal | author = Niv MY, Ripoll DR, Vila JA, Liwo A, Vanamee ES, Aggarwal AK, Weinstein H, Scheraga HA | title = Topology of Type II REases revisited; structural classes and the common conserved core | journal = NAR | volume = 35 | issue = 7 | pages = 2227–37 | year = 2007 | pmid = 17369272 | doi = 10.1093/nar/gkm045 | pmc = 1874628}} [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1874628&blobtype=pdf PDF]</ref> restriction endonuclease-like fold ({{SCOP|52979}}) and belongs to the large (more than 30 members) [[restriction endonuclease]] superfamily ({{SCOP|52980}}).<br /> <br /> ==Autoinhibition/activation mechanism==<br /> [[Structural alignment#Structural_superposition|Structure-based sequence]] alignment and [[site-directed mutagenesis]] identified the putative PD..D/EXK [[active site]]s of the EcoRII catalytic domain dimer that in apo structure are spatially blocked by the N-terminal domains.<ref name="Zhou_2004"/><br /> <br /> ==See also==<br /> *[[EcoRI]], another nuclease enzyme from ''[[Escherichia coli]]''.<br /> *[[EcoRV]], another nuclease enzyme from ''[[Escherichia coli]]''.<br /> *[[B3 DNA binding domain]] from [[higher plants]] is evolutionary related to EcoRII<br />  <br /> *[[FokI]], another nuclease enzyme from ''[[Flavobacterium okeanokoites]]''<br /> <br /> ==External links==<br /> *EcoRII in Restriction Enzyme Database [http://rebase.neb.com/rebase/enz/EcoRII.html REBASE]<br /> <br /> <br /> ==References==<br /> {{Reflist|2}}<br /> <br /> <references/><br /> <br /> ==Reference==<br /> <ref group="xtra">PMID:14659759</ref><references group="xtra"/><br /> [[Category: Escherichia coli]]<br /> [[Category: Type II site-specific deoxyribonuclease]]<br /> [[Category: Chen, L.]]announced<br /> [[Category: Kruger, D H.]]<br /> [[Category: Meehan, E J.]]<br /> [[Category: Mucke, M.]]<br /> [[Category: Reuter, M.]]<br /> [[Category: Wang, Y.]]<br /> [[Category: Zhou, X E.]]<br /> [[Category: Mutation]]<br /> [[Category: Replication]]<br /> [[Category: Site-specific restriction]]<br /> <br /> ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 03:36:10 2009''</div>

Dima Golovenko https://proteopedia.org/index.php?title=User:Dima_Golovenko/R.EcoRII&diff=1094229 User:Dima Golovenko/R.EcoRII 2010-06-11T15:43:23Z

<p>Dima Golovenko: /* Effector-binding domain */</p> <hr /> <div><br /> {{STRUCTURE_1na6| PDB=1na6 | SCENE= }} <br /> <br /> ===Crystal structure of restriction endonuclease EcoRII mutant R88A===<br /> <br /> <br /> {{ABSTRACT_PUBMED_14659759}}<br /> <br /> ==About this Structure==<br /> 1NA6 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NA6 OCA]. <br /> <br /> [[Restriction endonuclease]] (REase) '''EcoRII''' (pronounced "eco R two") is an [[enzyme]] of [[restriction modification system]] (RM) naturally found in ''[[Escherichia coli]]'', a [[Gram-negative bacteria]]. Its [[molecular mass]] is 45.2 [[Atomic mass unit|kDa]], being composed of 402 [[amino acids]].<ref name="title">{{cite web | url = http://rebase.neb.com/rebase/enz/EcoRII.html | title = EcoRII | accessdate = 2008-03-23 | author = Richard J. Roberts | authorlink = | coauthors = | date = | format = | work = REBASE - The Restriction Enzyme Database | publisher = | pages = | language = | archiveurl = | archivedate = | quote = }}</ref><br /> <br /> ==Mode of action==<br /> EcoRII is a [[bacterial]] Type IIE<ref name="pmid12654995">{{cite journal | author = Roberts RJ, Belfort M, Bestor T, ''et al.'' | title = A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes | journal = Nucleic Acids Res. | volume = 31 | issue = 7 | pages = 1805–12 | year = 2003 | pmid = 12654995 | doi = 10.1093/nar/gkg274 | pmc = 152790 }} [http://nar.oxfordjournals.org/cgi/reprint/31/7/1805.pdf PDF] </ref> [[restriction endonuclease|REase]] that interacts with two<ref name="pmid10903314">{{cite journal | author = Mücke M, Lurz R, Mackeldanz P, Behlke J, Krüger DH, Reuter M | title = Imaging DNA loops induced by restriction endonuclease EcoRII. A single amino acid substitution uncouples target recognition from cooperative DNA interaction and cleavage | journal = J. Biol. Chem. | volume = 275 | issue = 39 | pages = 30631–7 | year = 2000 | pmid = 10903314 | doi = 10.1074/jbc.M003904200 }}[http://www.jbc.org/cgi/reprint/275/39/30631.pdf PDF]</ref> or [http://pubs.acs.org/isubscribe/journals/bichaw/46/i39/figures/bi701123un00001.gif three]<ref name="pmid17845057">{{cite journal | author = Shlyakhtenko LS, Gilmore J, Portillo A, Tamulaitis G, Siksnys V, Lyubchenko YL | title = Direct visualization of the EcoRII-DNA triple synaptic complex by atomic force microscopy | journal = Biochemistry | volume = 46 | issue = 39 | pages = 11128–36 | year = 2007 | pmid = 17845057 | doi = 10.1021/bi701123u }}</ref> copies of the pseudopalindromic [[dsDNA|DNA]] [[Restriction_enzyme#Recognition_site|recognition sequence]] [[5' end|5']]-[[Cytosine|CC]]W[[Guanine|GG]]-[[3' end|3']] ([[W]] = [[Adenine|A]] or [[Thymine|T]]), one being the actual target of cleavage, the other(s) serving as the [[Allosteric regulation#Allosteric activation and inhibition|allosteric activator]](s). EcoRII cut target [[dsDNA|DNA]] sequence CCWGG generating [[sticky ends]].<ref name="isbn0-7167-3520-2">{{cite book | author = Griffiths, Anthony J. F. | title = An Introduction to genetic analysis | publisher = W.H. Freeman | location = San Francisco | year = 1999 | pages = | isbn = 0-7167-3520-2 | oclc = | doi = }}</ref><br /> <br /> ==Cut diagram==<br /> {| class="wikitable"<br /> | Recognition site<br /> | Cut results<br /> |- <br /> | <br /> 5' NN'''CCWGG'''NN<br /> 3' NN'''GGWCC'''NN <br /> |<br /> 5' NN '''CCWGG'''NN<br /> 3' NN'''GGWCC''' NN<br /> |}<br /> <br /> ==Structure==<br /> The [[apo]] [[X-ray crystallography|crystal]] [[protein structure|structure]] of EcoRII [[Point mutation|mutant]] R88A ({{PDB|1NA6}})<ref name="Zhou_2004">{{cite journal | author = Zhou XE, Wang Y, Reuter M, Mücke M, Krüger DH, Meehan EJ, Chen L | title = Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold | journal = J. Mol. Biol. | volume = 335 | issue = 1 | pages = 307–19 | year = 2004 | pmid = 14659759 | doi = 10.1016/j.jmb.2003.10.030 }}</ref> has been solved at 2.1 [[Å]] [[Resolution (electron density)|resolution]]. The EcoRII [[Primary structure|monomer]] has two [[Protein domains|domains]], [[N-terminus|N-terminal]] and [[C-terminus|C-terminal]], linked through a [[hinge]] [[turn (biochemistry)|loop]]. <br /> <br /> ===Effector-binding domain===<br /> <scene name='User:Dima_Golovenko/R.EcoRII/Effector_domain/1'>The N-terminal</scene> [[Effector (biology)|effector]]-[[DNA-binding domain|binding domain]] has a archetypal DNA-binding pseudobarrel fold ({{SCOP|101936}}) with a prominent [[structural motif|cleft]]. [[Structural alignment#DALI|Structural superposition]] showed it is evolutionarily related to:<br /> *[[B3 DNA binding domain]] ({{SCOP|117343}}) from the [[transcription factors]] in [[higher plants]] ({{PDB|1WID}})<ref name="pmid15548737">{{cite journal | author = Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Tomo Y, Hayami N, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S | title = Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1 | journal = Plant Cell | volume = 16 | issue = 12 | pages = 3448–59 | year = 2004 | pmid = 15548737 | doi = 10.1105/tpc.104.026112 | pmc = 535885 }}[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=535885&blobtype=pdf PDF]</ref><br /> *C-terminal domain of [[restriction endonuclease]] BfiI<ref name="BfiI">{{cite web | url = http://rebase.neb.com/rebase/enz/BfiI.html | title = BfiI | accessdate = 2008-03-23 | author = Richard J. Roberts | authorlink = | coauthors = | date = | format = | work = REBASE - The Restriction Enzyme Database | publisher = | pages = | language = | archiveurl = | archivedate = | quote = }}</ref> ({{PDB|2C1L}})<ref name="pmid16247004">{{cite journal | author = Grazulis S, Manakova E, Roessle M, Bochtler M, Tamulaitiene G, Huber R, Siksnys V | title = Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease | journal = Proc. Natl. Acad. Sci. U.S.A. | volume = 102 | issue = 44 | pages = 15797–802 | year = 2005 | pmid = 16247004 | doi = 10.1073/pnas.0507949102 | pmc = 1266039 }} [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1266039&blobtype=pdf PDF]</ref><br /> <br /> ===Catalytic domain===<br /> <scene name='User:Dima_Golovenko/R.EcoRII/Catalytic_domain/1'>The catalytic domain</scene> has a typical<ref name="pmid17369272">{{cite journal | author = Niv MY, Ripoll DR, Vila JA, Liwo A, Vanamee ES, Aggarwal AK, Weinstein H, Scheraga HA | title = Topology of Type II REases revisited; structural classes and the common conserved core | journal = NAR | volume = 35 | issue = 7 | pages = 2227–37 | year = 2007 | pmid = 17369272 | doi = 10.1093/nar/gkm045 | pmc = 1874628}} [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1874628&blobtype=pdf PDF]</ref> restriction endonuclease-like fold ({{SCOP|52979}}) and belongs to the large (more than 30 members) [[restriction endonuclease]] superfamily ({{SCOP|52980}}).<br /> <br /> ==Autoinhibition/activation mechanism==<br /> [[Structural alignment#Structural_superposition|Structure-based sequence]] alignment and [[site-directed mutagenesis]] identified the putative PD..D/EXK [[active site]]s of the EcoRII catalytic domain dimer that in apo structure are spatially blocked by the N-terminal domains.<ref name="Zhou_2004"/><br /> <br /> ==See also==<br /> *[[EcoRI]], another nuclease enzyme from ''[[Escherichia coli]]''.<br /> *[[EcoRV]], another nuclease enzyme from ''[[Escherichia coli]]''.<br /> *[[B3 DNA binding domain]] from [[higher plants]] is evolutionary related to EcoRII<br />  <br /> *[[FokI]], another nuclease enzyme from ''[[Flavobacterium okeanokoites]]''<br /> <br /> ==External links==<br /> *EcoRII in Restriction Enzyme Database [http://rebase.neb.com/rebase/enz/EcoRII.html REBASE]<br /> <br /> <br /> ==References==<br /> {{Reflist|2}}<br /> <br /> <references/><br /> <br /> ==Reference==<br /> <ref group="xtra">PMID:14659759</ref><references group="xtra"/><br /> [[Category: Escherichia coli]]<br /> [[Category: Type II site-specific deoxyribonuclease]]<br /> [[Category: Chen, L.]]announced<br /> [[Category: Kruger, D H.]]<br /> [[Category: Meehan, E J.]]<br /> [[Category: Mucke, M.]]<br /> [[Category: Reuter, M.]]<br /> [[Category: Wang, Y.]]<br /> [[Category: Zhou, X E.]]<br /> [[Category: Mutation]]<br /> [[Category: Replication]]<br /> [[Category: Site-specific restriction]]<br /> <br /> ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 03:36:10 2009''</div>

Dima Golovenko https://proteopedia.org/index.php?title=User:Dima_Golovenko/R.EcoRII&diff=1094228 User:Dima Golovenko/R.EcoRII 2010-06-11T15:42:58Z

<p>Dima Golovenko: /* Effector-binding domain */</p> <hr /> <div><br /> {{STRUCTURE_1na6| PDB=1na6 | SCENE= }} <br /> <br /> ===Crystal structure of restriction endonuclease EcoRII mutant R88A===<br /> <br /> <br /> {{ABSTRACT_PUBMED_14659759}}<br /> <br /> ==About this Structure==<br /> 1NA6 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NA6 OCA]. <br /> <br /> [[Restriction endonuclease]] (REase) '''EcoRII''' (pronounced "eco R two") is an [[enzyme]] of [[restriction modification system]] (RM) naturally found in ''[[Escherichia coli]]'', a [[Gram-negative bacteria]]. Its [[molecular mass]] is 45.2 [[Atomic mass unit|kDa]], being composed of 402 [[amino acids]].<ref name="title">{{cite web | url = http://rebase.neb.com/rebase/enz/EcoRII.html | title = EcoRII | accessdate = 2008-03-23 | author = Richard J. Roberts | authorlink = | coauthors = | date = | format = | work = REBASE - The Restriction Enzyme Database | publisher = | pages = | language = | archiveurl = | archivedate = | quote = }}</ref><br /> <br /> ==Mode of action==<br /> EcoRII is a [[bacterial]] Type IIE<ref name="pmid12654995">{{cite journal | author = Roberts RJ, Belfort M, Bestor T, ''et al.'' | title = A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes | journal = Nucleic Acids Res. | volume = 31 | issue = 7 | pages = 1805–12 | year = 2003 | pmid = 12654995 | doi = 10.1093/nar/gkg274 | pmc = 152790 }} [http://nar.oxfordjournals.org/cgi/reprint/31/7/1805.pdf PDF] </ref> [[restriction endonuclease|REase]] that interacts with two<ref name="pmid10903314">{{cite journal | author = Mücke M, Lurz R, Mackeldanz P, Behlke J, Krüger DH, Reuter M | title = Imaging DNA loops induced by restriction endonuclease EcoRII. A single amino acid substitution uncouples target recognition from cooperative DNA interaction and cleavage | journal = J. Biol. Chem. | volume = 275 | issue = 39 | pages = 30631–7 | year = 2000 | pmid = 10903314 | doi = 10.1074/jbc.M003904200 }}[http://www.jbc.org/cgi/reprint/275/39/30631.pdf PDF]</ref> or [http://pubs.acs.org/isubscribe/journals/bichaw/46/i39/figures/bi701123un00001.gif three]<ref name="pmid17845057">{{cite journal | author = Shlyakhtenko LS, Gilmore J, Portillo A, Tamulaitis G, Siksnys V, Lyubchenko YL | title = Direct visualization of the EcoRII-DNA triple synaptic complex by atomic force microscopy | journal = Biochemistry | volume = 46 | issue = 39 | pages = 11128–36 | year = 2007 | pmid = 17845057 | doi = 10.1021/bi701123u }}</ref> copies of the pseudopalindromic [[dsDNA|DNA]] [[Restriction_enzyme#Recognition_site|recognition sequence]] [[5' end|5']]-[[Cytosine|CC]]W[[Guanine|GG]]-[[3' end|3']] ([[W]] = [[Adenine|A]] or [[Thymine|T]]), one being the actual target of cleavage, the other(s) serving as the [[Allosteric regulation#Allosteric activation and inhibition|allosteric activator]](s). EcoRII cut target [[dsDNA|DNA]] sequence CCWGG generating [[sticky ends]].<ref name="isbn0-7167-3520-2">{{cite book | author = Griffiths, Anthony J. F. | title = An Introduction to genetic analysis | publisher = W.H. Freeman | location = San Francisco | year = 1999 | pages = | isbn = 0-7167-3520-2 | oclc = | doi = }}</ref><br /> <br /> ==Cut diagram==<br /> {| class="wikitable"<br /> | Recognition site<br /> | Cut results<br /> |- <br /> | <br /> 5' NN'''CCWGG'''NN<br /> 3' NN'''GGWCC'''NN <br /> |<br /> 5' NN '''CCWGG'''NN<br /> 3' NN'''GGWCC''' NN<br /> |}<br /> <br /> ==Structure==<br /> The [[apo]] [[X-ray crystallography|crystal]] [[protein structure|structure]] of EcoRII [[Point mutation|mutant]] R88A ({{PDB|1NA6}})<ref name="Zhou_2004">{{cite journal | author = Zhou XE, Wang Y, Reuter M, Mücke M, Krüger DH, Meehan EJ, Chen L | title = Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold | journal = J. Mol. Biol. | volume = 335 | issue = 1 | pages = 307–19 | year = 2004 | pmid = 14659759 | doi = 10.1016/j.jmb.2003.10.030 }}</ref> has been solved at 2.1 [[Å]] [[Resolution (electron density)|resolution]]. The EcoRII [[Primary structure|monomer]] has two [[Protein domains|domains]], [[N-terminus|N-terminal]] and [[C-terminus|C-terminal]], linked through a [[hinge]] [[turn (biochemistry)|loop]]. <br /> <br /> ===Effector-binding domain===<br /> <scene name='User:Dima_Golovenko/R.EcoRII/Effector_domain/1'>The N-terminal</scene>[[Effector (biology)|effector]]-[[DNA-binding domain|binding domain]] has a archetypal DNA-binding pseudobarrel fold ({{SCOP|101936}}) with a prominent [[structural motif|cleft]]. [[Structural alignment#DALI|Structural superposition]] showed it is evolutionarily related to:<br /> *[[B3 DNA binding domain]] ({{SCOP|117343}}) from the [[transcription factors]] in [[higher plants]] ({{PDB|1WID}})<ref name="pmid15548737">{{cite journal | author = Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Tomo Y, Hayami N, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S | title = Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1 | journal = Plant Cell | volume = 16 | issue = 12 | pages = 3448–59 | year = 2004 | pmid = 15548737 | doi = 10.1105/tpc.104.026112 | pmc = 535885 }}[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=535885&blobtype=pdf PDF]</ref><br /> *C-terminal domain of [[restriction endonuclease]] BfiI<ref name="BfiI">{{cite web | url = http://rebase.neb.com/rebase/enz/BfiI.html | title = BfiI | accessdate = 2008-03-23 | author = Richard J. Roberts | authorlink = | coauthors = | date = | format = | work = REBASE - The Restriction Enzyme Database | publisher = | pages = | language = | archiveurl = | archivedate = | quote = }}</ref> ({{PDB|2C1L}})<ref name="pmid16247004">{{cite journal | author = Grazulis S, Manakova E, Roessle M, Bochtler M, Tamulaitiene G, Huber R, Siksnys V | title = Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease | journal = Proc. Natl. Acad. Sci. U.S.A. | volume = 102 | issue = 44 | pages = 15797–802 | year = 2005 | pmid = 16247004 | doi = 10.1073/pnas.0507949102 | pmc = 1266039 }} [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1266039&blobtype=pdf PDF]</ref><br /> <br /> ===Catalytic domain===<br /> <scene name='User:Dima_Golovenko/R.EcoRII/Catalytic_domain/1'>The catalytic domain</scene> has a typical<ref name="pmid17369272">{{cite journal | author = Niv MY, Ripoll DR, Vila JA, Liwo A, Vanamee ES, Aggarwal AK, Weinstein H, Scheraga HA | title = Topology of Type II REases revisited; structural classes and the common conserved core | journal = NAR | volume = 35 | issue = 7 | pages = 2227–37 | year = 2007 | pmid = 17369272 | doi = 10.1093/nar/gkm045 | pmc = 1874628}} [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1874628&blobtype=pdf PDF]</ref> restriction endonuclease-like fold ({{SCOP|52979}}) and belongs to the large (more than 30 members) [[restriction endonuclease]] superfamily ({{SCOP|52980}}).<br /> <br /> ==Autoinhibition/activation mechanism==<br /> [[Structural alignment#Structural_superposition|Structure-based sequence]] alignment and [[site-directed mutagenesis]] identified the putative PD..D/EXK [[active site]]s of the EcoRII catalytic domain dimer that in apo structure are spatially blocked by the N-terminal domains.<ref name="Zhou_2004"/><br /> <br /> ==See also==<br /> *[[EcoRI]], another nuclease enzyme from ''[[Escherichia coli]]''.<br /> *[[EcoRV]], another nuclease enzyme from ''[[Escherichia coli]]''.<br /> *[[B3 DNA binding domain]] from [[higher plants]] is evolutionary related to EcoRII<br />  <br /> *[[FokI]], another nuclease enzyme from ''[[Flavobacterium okeanokoites]]''<br /> <br /> ==External links==<br /> *EcoRII in Restriction Enzyme Database [http://rebase.neb.com/rebase/enz/EcoRII.html REBASE]<br /> <br /> <br /> ==References==<br /> {{Reflist|2}}<br /> <br /> <references/><br /> <br /> ==Reference==<br /> <ref group="xtra">PMID:14659759</ref><references group="xtra"/><br /> [[Category: Escherichia coli]]<br /> [[Category: Type II site-specific deoxyribonuclease]]<br /> [[Category: Chen, L.]]announced<br /> [[Category: Kruger, D H.]]<br /> [[Category: Meehan, E J.]]<br /> [[Category: Mucke, M.]]<br /> [[Category: Reuter, M.]]<br /> [[Category: Wang, Y.]]<br /> [[Category: Zhou, X E.]]<br /> [[Category: Mutation]]<br /> [[Category: Replication]]<br /> [[Category: Site-specific restriction]]<br /> <br /> ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 03:36:10 2009''</div>

Dima Golovenko https://proteopedia.org/index.php?title=User:Dima_Golovenko/R.EcoRII&diff=1094227 User:Dima Golovenko/R.EcoRII 2010-06-11T15:38:55Z

<p>Dima Golovenko: /* Catalytic domain */</p> <hr /> <div><br /> {{STRUCTURE_1na6| PDB=1na6 | SCENE= }} <br /> <br /> ===Crystal structure of restriction endonuclease EcoRII mutant R88A===<br /> <br /> <br /> {{ABSTRACT_PUBMED_14659759}}<br /> <br /> ==About this Structure==<br /> 1NA6 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NA6 OCA]. <br /> <br /> [[Restriction endonuclease]] (REase) '''EcoRII''' (pronounced "eco R two") is an [[enzyme]] of [[restriction modification system]] (RM) naturally found in ''[[Escherichia coli]]'', a [[Gram-negative bacteria]]. Its [[molecular mass]] is 45.2 [[Atomic mass unit|kDa]], being composed of 402 [[amino acids]].<ref name="title">{{cite web | url = http://rebase.neb.com/rebase/enz/EcoRII.html | title = EcoRII | accessdate = 2008-03-23 | author = Richard J. Roberts | authorlink = | coauthors = | date = | format = | work = REBASE - The Restriction Enzyme Database | publisher = | pages = | language = | archiveurl = | archivedate = | quote = }}</ref><br /> <br /> ==Mode of action==<br /> EcoRII is a [[bacterial]] Type IIE<ref name="pmid12654995">{{cite journal | author = Roberts RJ, Belfort M, Bestor T, ''et al.'' | title = A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes | journal = Nucleic Acids Res. | volume = 31 | issue = 7 | pages = 1805–12 | year = 2003 | pmid = 12654995 | doi = 10.1093/nar/gkg274 | pmc = 152790 }} [http://nar.oxfordjournals.org/cgi/reprint/31/7/1805.pdf PDF] </ref> [[restriction endonuclease|REase]] that interacts with two<ref name="pmid10903314">{{cite journal | author = Mücke M, Lurz R, Mackeldanz P, Behlke J, Krüger DH, Reuter M | title = Imaging DNA loops induced by restriction endonuclease EcoRII. A single amino acid substitution uncouples target recognition from cooperative DNA interaction and cleavage | journal = J. Biol. Chem. | volume = 275 | issue = 39 | pages = 30631–7 | year = 2000 | pmid = 10903314 | doi = 10.1074/jbc.M003904200 }}[http://www.jbc.org/cgi/reprint/275/39/30631.pdf PDF]</ref> or [http://pubs.acs.org/isubscribe/journals/bichaw/46/i39/figures/bi701123un00001.gif three]<ref name="pmid17845057">{{cite journal | author = Shlyakhtenko LS, Gilmore J, Portillo A, Tamulaitis G, Siksnys V, Lyubchenko YL | title = Direct visualization of the EcoRII-DNA triple synaptic complex by atomic force microscopy | journal = Biochemistry | volume = 46 | issue = 39 | pages = 11128–36 | year = 2007 | pmid = 17845057 | doi = 10.1021/bi701123u }}</ref> copies of the pseudopalindromic [[dsDNA|DNA]] [[Restriction_enzyme#Recognition_site|recognition sequence]] [[5' end|5']]-[[Cytosine|CC]]W[[Guanine|GG]]-[[3' end|3']] ([[W]] = [[Adenine|A]] or [[Thymine|T]]), one being the actual target of cleavage, the other(s) serving as the [[Allosteric regulation#Allosteric activation and inhibition|allosteric activator]](s). EcoRII cut target [[dsDNA|DNA]] sequence CCWGG generating [[sticky ends]].<ref name="isbn0-7167-3520-2">{{cite book | author = Griffiths, Anthony J. F. | title = An Introduction to genetic analysis | publisher = W.H. Freeman | location = San Francisco | year = 1999 | pages = | isbn = 0-7167-3520-2 | oclc = | doi = }}</ref><br /> <br /> ==Cut diagram==<br /> {| class="wikitable"<br /> | Recognition site<br /> | Cut results<br /> |- <br /> | <br /> 5' NN'''CCWGG'''NN<br /> 3' NN'''GGWCC'''NN <br /> |<br /> 5' NN '''CCWGG'''NN<br /> 3' NN'''GGWCC''' NN<br /> |}<br /> <br /> ==Structure==<br /> The [[apo]] [[X-ray crystallography|crystal]] [[protein structure|structure]] of EcoRII [[Point mutation|mutant]] R88A ({{PDB|1NA6}})<ref name="Zhou_2004">{{cite journal | author = Zhou XE, Wang Y, Reuter M, Mücke M, Krüger DH, Meehan EJ, Chen L | title = Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold | journal = J. Mol. Biol. | volume = 335 | issue = 1 | pages = 307–19 | year = 2004 | pmid = 14659759 | doi = 10.1016/j.jmb.2003.10.030 }}</ref> has been solved at 2.1 [[Å]] [[Resolution (electron density)|resolution]]. The EcoRII [[Primary structure|monomer]] has two [[Protein domains|domains]], [[N-terminus|N-terminal]] and [[C-terminus|C-terminal]], linked through a [[hinge]] [[turn (biochemistry)|loop]]. <br /> <br /> ===Effector-binding domain===<br /> The N-terminal [[Effector (biology)|effector]]-[[DNA-binding domain|binding domain]] has a archetypal DNA-binding pseudobarrel fold ({{SCOP|101936}}) with a prominent [[structural motif|cleft]]. [[Structural alignment#DALI|Structural superposition]] showed it is evolutionarily related to:<br /> *[[B3 DNA binding domain]] ({{SCOP|117343}}) from the [[transcription factors]] in [[higher plants]] ({{PDB|1WID}})<ref name="pmid15548737">{{cite journal | author = Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Tomo Y, Hayami N, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S | title = Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1 | journal = Plant Cell | volume = 16 | issue = 12 | pages = 3448–59 | year = 2004 | pmid = 15548737 | doi = 10.1105/tpc.104.026112 | pmc = 535885 }}[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=535885&blobtype=pdf PDF]</ref><br /> *C-terminal domain of [[restriction endonuclease]] BfiI<ref name="BfiI">{{cite web | url = http://rebase.neb.com/rebase/enz/BfiI.html | title = BfiI | accessdate = 2008-03-23 | author = Richard J. Roberts | authorlink = | coauthors = | date = | format = | work = REBASE - The Restriction Enzyme Database | publisher = | pages = | language = | archiveurl = | archivedate = | quote = }}</ref> ({{PDB|2C1L}})<ref name="pmid16247004">{{cite journal | author = Grazulis S, Manakova E, Roessle M, Bochtler M, Tamulaitiene G, Huber R, Siksnys V | title = Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease | journal = Proc. Natl. Acad. Sci. U.S.A. | volume = 102 | issue = 44 | pages = 15797–802 | year = 2005 | pmid = 16247004 | doi = 10.1073/pnas.0507949102 | pmc = 1266039 }} [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1266039&blobtype=pdf PDF]</ref><br /> <br /> ===Catalytic domain===<br /> <scene name='User:Dima_Golovenko/R.EcoRII/Catalytic_domain/1'>The catalytic domain</scene> has a typical<ref name="pmid17369272">{{cite journal | author = Niv MY, Ripoll DR, Vila JA, Liwo A, Vanamee ES, Aggarwal AK, Weinstein H, Scheraga HA | title = Topology of Type II REases revisited; structural classes and the common conserved core | journal = NAR | volume = 35 | issue = 7 | pages = 2227–37 | year = 2007 | pmid = 17369272 | doi = 10.1093/nar/gkm045 | pmc = 1874628}} [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1874628&blobtype=pdf PDF]</ref> restriction endonuclease-like fold ({{SCOP|52979}}) and belongs to the large (more than 30 members) [[restriction endonuclease]] superfamily ({{SCOP|52980}}).<br /> <br /> ==Autoinhibition/activation mechanism==<br /> [[Structural alignment#Structural_superposition|Structure-based sequence]] alignment and [[site-directed mutagenesis]] identified the putative PD..D/EXK [[active site]]s of the EcoRII catalytic domain dimer that in apo structure are spatially blocked by the N-terminal domains.<ref name="Zhou_2004"/><br /> <br /> ==See also==<br /> *[[EcoRI]], another nuclease enzyme from ''[[Escherichia coli]]''.<br /> *[[EcoRV]], another nuclease enzyme from ''[[Escherichia coli]]''.<br /> *[[B3 DNA binding domain]] from [[higher plants]] is evolutionary related to EcoRII<br />  <br /> *[[FokI]], another nuclease enzyme from ''[[Flavobacterium okeanokoites]]''<br /> <br /> ==External links==<br /> *EcoRII in Restriction Enzyme Database [http://rebase.neb.com/rebase/enz/EcoRII.html REBASE]<br /> <br /> <br /> ==References==<br /> {{Reflist|2}}<br /> <br /> <references/><br /> <br /> ==Reference==<br /> <ref group="xtra">PMID:14659759</ref><references group="xtra"/><br /> [[Category: Escherichia coli]]<br /> [[Category: Type II site-specific deoxyribonuclease]]<br /> [[Category: Chen, L.]]announced<br /> [[Category: Kruger, D H.]]<br /> [[Category: Meehan, E J.]]<br /> [[Category: Mucke, M.]]<br /> [[Category: Reuter, M.]]<br /> [[Category: Wang, Y.]]<br /> [[Category: Zhou, X E.]]<br /> [[Category: Mutation]]<br /> [[Category: Replication]]<br /> [[Category: Site-specific restriction]]<br /> <br /> ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 03:36:10 2009''</div>

Dima Golovenko https://proteopedia.org/index.php?title=User:Dima_Golovenko/R.EcoRII&diff=1094226 User:Dima Golovenko/R.EcoRII 2010-06-11T15:28:26Z

<p>Dima Golovenko: </p> <hr /> <div><br /> {{STRUCTURE_1na6| PDB=1na6 | SCENE= }} <br /> <br /> ===Crystal structure of restriction endonuclease EcoRII mutant R88A===<br /> <br /> <br /> {{ABSTRACT_PUBMED_14659759}}<br /> <br /> ==About this Structure==<br /> 1NA6 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NA6 OCA]. <br /> <br /> [[Restriction endonuclease]] (REase) '''EcoRII''' (pronounced "eco R two") is an [[enzyme]] of [[restriction modification system]] (RM) naturally found in ''[[Escherichia coli]]'', a [[Gram-negative bacteria]]. Its [[molecular mass]] is 45.2 [[Atomic mass unit|kDa]], being composed of 402 [[amino acids]].<ref name="title">{{cite web | url = http://rebase.neb.com/rebase/enz/EcoRII.html | title = EcoRII | accessdate = 2008-03-23 | author = Richard J. Roberts | authorlink = | coauthors = | date = | format = | work = REBASE - The Restriction Enzyme Database | publisher = | pages = | language = | archiveurl = | archivedate = | quote = }}</ref><br /> <br /> ==Mode of action==<br /> EcoRII is a [[bacterial]] Type IIE<ref name="pmid12654995">{{cite journal | author = Roberts RJ, Belfort M, Bestor T, ''et al.'' | title = A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes | journal = Nucleic Acids Res. | volume = 31 | issue = 7 | pages = 1805–12 | year = 2003 | pmid = 12654995 | doi = 10.1093/nar/gkg274 | pmc = 152790 }} [http://nar.oxfordjournals.org/cgi/reprint/31/7/1805.pdf PDF] </ref> [[restriction endonuclease|REase]] that interacts with two<ref name="pmid10903314">{{cite journal | author = Mücke M, Lurz R, Mackeldanz P, Behlke J, Krüger DH, Reuter M | title = Imaging DNA loops induced by restriction endonuclease EcoRII. A single amino acid substitution uncouples target recognition from cooperative DNA interaction and cleavage | journal = J. Biol. Chem. | volume = 275 | issue = 39 | pages = 30631–7 | year = 2000 | pmid = 10903314 | doi = 10.1074/jbc.M003904200 }}[http://www.jbc.org/cgi/reprint/275/39/30631.pdf PDF]</ref> or [http://pubs.acs.org/isubscribe/journals/bichaw/46/i39/figures/bi701123un00001.gif three]<ref name="pmid17845057">{{cite journal | author = Shlyakhtenko LS, Gilmore J, Portillo A, Tamulaitis G, Siksnys V, Lyubchenko YL | title = Direct visualization of the EcoRII-DNA triple synaptic complex by atomic force microscopy | journal = Biochemistry | volume = 46 | issue = 39 | pages = 11128–36 | year = 2007 | pmid = 17845057 | doi = 10.1021/bi701123u }}</ref> copies of the pseudopalindromic [[dsDNA|DNA]] [[Restriction_enzyme#Recognition_site|recognition sequence]] [[5' end|5']]-[[Cytosine|CC]]W[[Guanine|GG]]-[[3' end|3']] ([[W]] = [[Adenine|A]] or [[Thymine|T]]), one being the actual target of cleavage, the other(s) serving as the [[Allosteric regulation#Allosteric activation and inhibition|allosteric activator]](s). EcoRII cut target [[dsDNA|DNA]] sequence CCWGG generating [[sticky ends]].<ref name="isbn0-7167-3520-2">{{cite book | author = Griffiths, Anthony J. F. | title = An Introduction to genetic analysis | publisher = W.H. Freeman | location = San Francisco | year = 1999 | pages = | isbn = 0-7167-3520-2 | oclc = | doi = }}</ref><br /> <br /> ==Cut diagram==<br /> {| class="wikitable"<br /> | Recognition site<br /> | Cut results<br /> |- <br /> | <br /> 5' NN'''CCWGG'''NN<br /> 3' NN'''GGWCC'''NN <br /> |<br /> 5' NN '''CCWGG'''NN<br /> 3' NN'''GGWCC''' NN<br /> |}<br /> <br /> ==Structure==<br /> The [[apo]] [[X-ray crystallography|crystal]] [[protein structure|structure]] of EcoRII [[Point mutation|mutant]] R88A ({{PDB|1NA6}})<ref name="Zhou_2004">{{cite journal | author = Zhou XE, Wang Y, Reuter M, Mücke M, Krüger DH, Meehan EJ, Chen L | title = Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold | journal = J. Mol. Biol. | volume = 335 | issue = 1 | pages = 307–19 | year = 2004 | pmid = 14659759 | doi = 10.1016/j.jmb.2003.10.030 }}</ref> has been solved at 2.1 [[Å]] [[Resolution (electron density)|resolution]]. The EcoRII [[Primary structure|monomer]] has two [[Protein domains|domains]], [[N-terminus|N-terminal]] and [[C-terminus|C-terminal]], linked through a [[hinge]] [[turn (biochemistry)|loop]]. <br /> <br /> ===Effector-binding domain===<br /> The N-terminal [[Effector (biology)|effector]]-[[DNA-binding domain|binding domain]] has a archetypal DNA-binding pseudobarrel fold ({{SCOP|101936}}) with a prominent [[structural motif|cleft]]. [[Structural alignment#DALI|Structural superposition]] showed it is evolutionarily related to:<br /> *[[B3 DNA binding domain]] ({{SCOP|117343}}) from the [[transcription factors]] in [[higher plants]] ({{PDB|1WID}})<ref name="pmid15548737">{{cite journal | author = Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Tomo Y, Hayami N, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S | title = Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1 | journal = Plant Cell | volume = 16 | issue = 12 | pages = 3448–59 | year = 2004 | pmid = 15548737 | doi = 10.1105/tpc.104.026112 | pmc = 535885 }}[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=535885&blobtype=pdf PDF]</ref><br /> *C-terminal domain of [[restriction endonuclease]] BfiI<ref name="BfiI">{{cite web | url = http://rebase.neb.com/rebase/enz/BfiI.html | title = BfiI | accessdate = 2008-03-23 | author = Richard J. Roberts | authorlink = | coauthors = | date = | format = | work = REBASE - The Restriction Enzyme Database | publisher = | pages = | language = | archiveurl = | archivedate = | quote = }}</ref> ({{PDB|2C1L}})<ref name="pmid16247004">{{cite journal | author = Grazulis S, Manakova E, Roessle M, Bochtler M, Tamulaitiene G, Huber R, Siksnys V | title = Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease | journal = Proc. Natl. Acad. Sci. U.S.A. | volume = 102 | issue = 44 | pages = 15797–802 | year = 2005 | pmid = 16247004 | doi = 10.1073/pnas.0507949102 | pmc = 1266039 }} [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1266039&blobtype=pdf PDF]</ref><br /> <br /> ===Catalytic domain===<br /> <scene name='1na6/C-term/1'>The C-terminal domain</scene> has a typical<ref name="pmid17369272">{{cite journal | author = Niv MY, Ripoll DR, Vila JA, Liwo A, Vanamee ES, Aggarwal AK, Weinstein H, Scheraga HA | title = Topology of Type II REases revisited; structural classes and the common conserved core | journal = NAR | volume = 35 | issue = 7 | pages = 2227–37 | year = 2007 | pmid = 17369272 | doi = 10.1093/nar/gkm045 | pmc = 1874628}} [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1874628&blobtype=pdf PDF]</ref> restriction endonuclease-like fold ({{SCOP|52979}}) and belongs to the large (more than 30 members) [[restriction endonuclease]] superfamily ({{SCOP|52980}}).<br /> <br /> ==Autoinhibition/activation mechanism==<br /> [[Structural alignment#Structural_superposition|Structure-based sequence]] alignment and [[site-directed mutagenesis]] identified the putative PD..D/EXK [[active site]]s of the EcoRII catalytic domain dimer that in apo structure are spatially blocked by the N-terminal domains.<ref name="Zhou_2004"/><br /> <br /> ==See also==<br /> *[[EcoRI]], another nuclease enzyme from ''[[Escherichia coli]]''.<br /> *[[EcoRV]], another nuclease enzyme from ''[[Escherichia coli]]''.<br /> *[[B3 DNA binding domain]] from [[higher plants]] is evolutionary related to EcoRII<br />  <br /> *[[FokI]], another nuclease enzyme from ''[[Flavobacterium okeanokoites]]''<br /> <br /> ==External links==<br /> *EcoRII in Restriction Enzyme Database [http://rebase.neb.com/rebase/enz/EcoRII.html REBASE]<br /> <br /> <br /> ==References==<br /> {{Reflist|2}}<br /> <br /> <references/><br /> <br /> ==Reference==<br /> <ref group="xtra">PMID:14659759</ref><references group="xtra"/><br /> [[Category: Escherichia coli]]<br /> [[Category: Type II site-specific deoxyribonuclease]]<br /> [[Category: Chen, L.]]announced<br /> [[Category: Kruger, D H.]]<br /> [[Category: Meehan, E J.]]<br /> [[Category: Mucke, M.]]<br /> [[Category: Reuter, M.]]<br /> [[Category: Wang, Y.]]<br /> [[Category: Zhou, X E.]]<br /> [[Category: Mutation]]<br /> [[Category: Replication]]<br /> [[Category: Site-specific restriction]]<br /> <br /> ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 03:36:10 2009''</div>

Dima Golovenko https://proteopedia.org/index.php?title=User:Dima_Golovenko/R.EcoRII&diff=1094223 User:Dima Golovenko/R.EcoRII 2010-06-11T15:27:04Z

<p>Dima Golovenko: New page: ==This is a placeholder== This is a placeholder text to help you get started in placing a Jmol applet on your page. At any time, click "Show Preview" at the bottom of this page to see how...</p> <hr /> <div>==This is a placeholder==<br /> This is a placeholder text to help you get started in <br /> placing a Jmol applet on your page. At any time, click<br /> "Show Preview" at the bottom of this page to see how it goes.<br /> <br /> Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load <br /> and display another structure.<br /> <br /> {{STRUCTURE_1na6 | PDB=1na6 | SCENE= }}</div>

Dima Golovenko https://proteopedia.org/index.php?title=Sandbox_erice_4&diff=1092589 Sandbox erice 4 2010-06-09T12:50:06Z

<p>Dima Golovenko: </p> <hr /> <div>[[Image:3cl0 Erice 2.png|thumb|left|150px|Influenza neuraminidase(3cl0)]]<br /> <br /> '''Influenza neuraminidase''' is a glycoprotein in the influenza virus membrane. Before an infected cell can release the virus into its surroundings to infect new cells, neuraminidase must cleave sialic acid from both virus and cellular glycoproteins. Neuraminidase is a homotetramer -- here we will examine only one monomer.<br /> <br /> <br /> == Exploring the Structure ==<br /> <br /> <applet load='3cl0' size='300' frame='true' align='right' caption='Insert caption here' /><br /> <br /> Because of its important role in virus infectivity, several anti-viral drugs have been designed to target neuraminidase, including <scene name='Sandbox_erice_4/Zoom_3cl0/1'>oseltamavir</scene> (Tamiflu) and zanamivir (Relenza). Oseltamavir binding to neuraminidase moves glutamate 276 towards histidine 274, making more room for oseltamavir to bind tightly (PDB entry [[2hu4]]). But, in a common mutant (H274Y), a larger tyrosine replaces the smaller histidine 274, preventing glutamate 276 from moving to make room for oseltamavir binding, resulting in weaker drug binding and thus resistance (PDB entry [[3cl0]]). Luckily the H274Y neuraminidase mutant is still susceptible to zanamivir, which is smaller than oseltamavir. <br /> <ref>pmid:18480754</ref><br /> <br /> <scene name='Sandbox_erice_4/Scene_1/1'>TextToBeDisplayed</scene><br /> <br /> <scene name='Sandbox_erice_4/Common_mutants_2/1'>common mutant Y274</scene><br /> <br /> <br /> <references/></div>

Dima Golovenko https://proteopedia.org/index.php?title=Sandbox_erice_4&diff=1092585 Sandbox erice 4 2010-06-09T12:47:57Z

<p>Dima Golovenko: </p> <hr /> <div>[[Image:3cl0 Erice 2.png|thumb|left|150px|Influenza neuraminidase(3cl0)]]<br /> <br /> '''Influenza neuraminidase''' is a glycoprotein in the influenza virus membrane. Before an infected cell can release the virus into its surroundings to infect new cells, neuraminidase must cleave sialic acid from both virus and cellular glycoproteins. Neuraminidase is a homotetramer -- here we will examine only one monomer.<br /> <br /> <br /> == Exploring the Structure ==<br /> <br /> <applet load='3cl0' size='300' frame='true' align='right' caption='Insert caption here' /><br /> <br /> Because of its important role in virus infectivity, several anti-viral drugs have been designed to target neuraminidase, including <scene name='Sandbox_erice_4/Zoom_3cl0/1'>oseltamavir</scene> (Tamiflu) and zanamivir (Relenza). Oseltamavir binding to neuraminidase moves glutamate 276 towards histidine 274, making more room for oseltamavir to bind tightly (PDB entry [[2hu4]]). But, in a common mutant (H274Y), a larger tyrosine replaces the smaller histidine 274, preventing glutamate 276 from moving to make room for oseltamavir binding, resulting in weaker drug binding and thus resistance (PDB entry [[3cl0]]). Luckily the H274Y neuraminidase mutant is still susceptible to zanamivir, which is smaller than oseltamavir.<br /> <br /> <scene name='Sandbox_erice_4/Scene_1/1'>TextToBeDisplayed</scene><br /> <br /> <scene name='Sandbox_erice_4/Common_mutants_2/1'>common mutant Y274</scene><br /> <br /> <references/><br /> <br /> <ref>pmid:18480754</ref></div>

Dima Golovenko https://proteopedia.org/index.php?title=Sandbox_erice_4&diff=1092584 Sandbox erice 4 2010-06-09T12:47:23Z

<p>Dima Golovenko: </p> <hr /> <div>[[Image:3cl0 Erice 2.png|thumb|left|150px|Influenza neuraminidase(3cl0)]]<br /> <br /> '''Influenza nhttp://www.proteopedia.org/wiki/skins/common/images/button_sig.pngeuraminidase''' is a glycoprotein in the influenza virus membrane. Before an infected cell can release the virus into its surroundings to infect new cells, neuraminidase must cleave sialic acid from both virus and cellular glycoproteins. Neuraminidase is a homotetramer -- here we will examine only one monomer.<br /> <br /> <br /> == Exploring the Structure ==<br /> <br /> <applet load='3cl0' size='300' frame='true' align='right' caption='Insert caption here' /><br /> <br /> Because of its important role in virus infectivity, several anti-viral drugs have been designed to target neuraminidase, including <scene name='Sandbox_erice_4/Zoom_3cl0/1'>oseltamavir</scene> (Tamiflu) and zanamivir (Relenza). Oseltamavir binding to neuraminidase moves glutamate 276 towards histidine 274, making more room for oseltamavir to bind tightly (PDB entry [[2hu4]]). But, in a common mutant (H274Y), a larger tyrosine replaces the smaller histidine 274, preventing glutamate 276 from moving to make room for oseltamavir binding, resulting in weaker drug binding and thus resistance (PDB entry [[3cl0]]). Luckily the H274Y neuraminidase mutant is still susceptible to zanamivir, which is smaller than oseltamavir.<br /> <br /> <scene name='Sandbox_erice_4/Scene_1/1'>TextToBeDisplayed</scene><br /> <br /> <scene name='Sandbox_erice_4/Common_mutants_2/1'>common mutant Y274</scene><br /> <br /> <references/><br /> <br /> <ref>pmid:18480754</ref></div>

Dima Golovenko https://proteopedia.org/index.php?title=Sandbox_erice_4&diff=1092583 Sandbox erice 4 2010-06-09T12:46:41Z

<p>Dima Golovenko: </p> <hr /> <div>[[Image:3cl0 Erice 2.png|thumb|left|150px|Influenza neuraminidase(3cl0)]]<br /> <br /> '''Influenza nhttp://www.proteopedia.org/wiki/skins/common/images/button_sig.pngeuraminidase''' is a glycoprotein in the influenza virus membrane. Before an infected cell can release the virus into its surroundings to infect new cells, neuraminidase must cleave sialic acid from both virus and cellular glycoproteins. Neuraminidase is a homotetramer -- here we will examine only one monomer.<br /> <br /> <br /> == Exploring the Structure ==<br /> <br /> <applet load='3cl0' size='300' frame='true' align='right' caption='Insert caption here' /><br /> <br /> Because of its important role in virus infectivity, several anti-viral drugs have been designed to target neuraminidase, including <scene name='Sandbox_erice_4/Zoom_3cl0/1'>oseltamavir</scene> (Tamiflu) and zanamivir (Relenza). Oseltamavir binding to neuraminidase moves glutamate 276 towards histidine 274, making more room for oseltamavir to bind tightly (PDB entry [[2hu4]]). But, in a common mutant (H274Y), a larger tyrosine replaces the smaller histidine 274, preventing glutamate 276 from moving to make room for oseltamavir binding, resulting in weaker drug binding and thus resistance (PDB entry [[3cl0]]). Luckily the H274Y neuraminidase mutant is still susceptible to zanamivir, which is smaller than oseltamavir.<br /> <ref>pmid:18480754</ref><br /> <br /> <scene name='Sandbox_erice_4/Scene_1/1'>TextToBeDisplayed</scene><br /> <br /> <scene name='Sandbox_erice_4/Common_mutants_2/1'>common mutant Y274</scene><br /> <br /> <references/></div>

Dima Golovenko https://proteopedia.org/index.php?title=Sandbox_erice_4&diff=1092580 Sandbox erice 4 2010-06-09T12:45:55Z

<p>Dima Golovenko: </p> <hr /> <div>[[Image:3cl0 Erice 2.png|thumb|left|150px|Influenza neuraminidase]]<br /> <br /> '''Influenza nhttp://www.proteopedia.org/wiki/skins/common/images/button_sig.pngeuraminidase''' is a glycoprotein in the influenza virus membrane. Before an infected cell can release the virus into its surroundings to infect new cells, neuraminidase must cleave sialic acid from both virus and cellular glycoproteins. Neuraminidase is a homotetramer -- here we will examine only one monomer.<br /> <br /> <br /> == Exploring the Structure ==<br /> <br /> <applet load='3cl0' size='300' frame='true' align='right' caption='Insert caption here' /><br /> <br /> Because of its important role in virus infectivity, several anti-viral drugs have been designed to target neuraminidase, including <scene name='Sandbox_erice_4/Zoom_3cl0/1'>oseltamavir</scene> (Tamiflu) and zanamivir (Relenza). Oseltamavir binding to neuraminidase moves glutamate 276 towards histidine 274, making more room for oseltamavir to bind tightly (PDB entry [[2hu4]]). But, in a common mutant (H274Y), a larger tyrosine replaces the smaller histidine 274, preventing glutamate 276 from moving to make room for oseltamavir binding, resulting in weaker drug binding and thus resistance (PDB entry [[3cl0]]). Luckily the H274Y neuraminidase mutant is still susceptible to zanamivir, which is smaller than oseltamavir.<br /> <ref>pmid:18480754</ref><br /> <br /> <scene name='Sandbox_erice_4/Scene_1/1'>TextToBeDisplayed</scene><br /> <br /> <scene name='Sandbox_erice_4/Common_mutants_2/1'>common mutant Y274</scene><br /> <br /> <references/></div>

Dima Golovenko https://proteopedia.org/index.php?title=Sandbox_erice_4&diff=1092578 Sandbox erice 4 2010-06-09T12:41:26Z

<p>Dima Golovenko: </p> <hr /> <div>[[Image:3cl0 Erice 2.png]]<br /> <br /> '''Influenza nhttp://www.proteopedia.org/wiki/skins/common/images/button_sig.pngeuraminidase''' is a glycoprotein in the influenza virus membrane. Before an infected cell can release the virus into its surroundings to infect new cells, neuraminidase must cleave sialic acid from both virus and cellular glycoproteins. Neuraminidase is a homotetramer -- here we will examine only one monomer.<br /> <br /> <br /> == Exploring the Structure ==<br /> <br /> <applet load='3cl0' size='300' frame='true' align='right' caption='Insert caption here' /><br /> <br /> Because of its important role in virus infectivity, several anti-viral drugs have been designed to target neuraminidase, including <scene name='Sandbox_erice_4/Zoom_3cl0/1'>oseltamavir</scene> (Tamiflu) and zanamivir (Relenza). Oseltamavir binding to neuraminidase moves glutamate 276 towards histidine 274, making more room for oseltamavir to bind tightly (PDB entry [[2hu4]]). But, in a common mutant (H274Y), a larger tyrosine replaces the smaller histidine 274, preventing glutamate 276 from moving to make room for oseltamavir binding, resulting in weaker drug binding and thus resistance (PDB entry [[3cl0]]). Luckily the H274Y neuraminidase mutant is still susceptible to zanamivir, which is smaller than oseltamavir.<br /> <ref>pmid:18480754</ref><br /> <br /> <scene name='Sandbox_erice_4/Scene_1/1'>TextToBeDisplayed</scene><br /> <br /> <scene name='Sandbox_erice_4/Common_mutants_2/1'>common mutant Y274</scene><br /> <br /> <references/></div>

Dima Golovenko https://proteopedia.org/index.php?title=Sandbox_erice_4&diff=1092574 Sandbox erice 4 2010-06-09T12:40:21Z

<p>Dima Golovenko: </p> <hr /> <div>[[Image:3cl0 Erice 4.jpg]]<br /> <br /> '''Influenza neuraminidase''' is a glycoprotein in the influenza virus membrane. Before an infected cell can release the virus into its surroundings to infect new cells, neuraminidase must cleave sialic acid from both virus and cellular glycoproteins. Neuraminidase is a homotetramer -- here we will examine only one monomer.<br /> <br /> <br /> == Exploring the Structure ==<br /> <br /> <applet load='3cl0' size='300' frame='true' align='right' caption='Insert caption here' /><br /> <br /> Because of its important role in virus infectivity, several anti-viral drugs have been designed to target neuraminidase, including <scene name='Sandbox_erice_4/Zoom_3cl0/1'>oseltamavir</scene> (Tamiflu) and zanamivir (Relenza). Oseltamavir binding to neuraminidase moves glutamate 276 towards histidine 274, making more room for oseltamavir to bind tightly (PDB entry [[2hu4]]). But, in a common mutant (H274Y), a larger tyrosine replaces the smaller histidine 274, preventing glutamate 276 from moving to make room for oseltamavir binding, resulting in weaker drug binding and thus resistance (PDB entry [[3cl0]]). Luckily the H274Y neuraminidase mutant is still susceptible to zanamivir, which is smaller than oseltamavir.<br /> <ref>pmid:18480754</ref><br /> <br /> <scene name='Sandbox_erice_4/Scene_1/1'>TextToBeDisplayed</scene><br /> <br /> <scene name='Sandbox_erice_4/Common_mutants_2/1'>common mutant Y274</scene><br /> <br /> <references/></div>

Dima Golovenko https://proteopedia.org/index.php?title=Sandbox_erice_4&diff=1092573 Sandbox erice 4 2010-06-09T12:40:03Z

<p>Dima Golovenko: /* Exploring the Structure */</p> <hr /> <div>[[Image:3cl0 Erice 1.jpg]]<br /> <br /> '''Influenza neuraminidase''' is a glycoprotein in the influenza virus membrane. Before an infected cell can release the virus into its surroundings to infect new cells, neuraminidase must cleave sialic acid from both virus and cellular glycoproteins. Neuraminidase is a homotetramer -- here we will examine only one monomer.<br /> <br /> <br /> == Exploring the Structure ==<br /> <br /> <applet load='3cl0' size='300' frame='true' align='right' caption='Insert caption here' /><br /> <br /> Because of its important role in virus infectivity, several anti-viral drugs have been designed to target neuraminidase, including <scene name='Sandbox_erice_4/Zoom_3cl0/1'>oseltamavir</scene> (Tamiflu) and zanamivir (Relenza). Oseltamavir binding to neuraminidase moves glutamate 276 towards histidine 274, making more room for oseltamavir to bind tightly (PDB entry [[2hu4]]). But, in a common mutant (H274Y), a larger tyrosine replaces the smaller histidine 274, preventing glutamate 276 from moving to make room for oseltamavir binding, resulting in weaker drug binding and thus resistance (PDB entry [[3cl0]]). Luckily the H274Y neuraminidase mutant is still susceptible to zanamivir, which is smaller than oseltamavir.<br /> <ref>pmid:18480754</ref><br /> <br /> <scene name='Sandbox_erice_4/Scene_1/1'>TextToBeDisplayed</scene><br /> <br /> <scene name='Sandbox_erice_4/Common_mutants_2/1'>common mutant Y274</scene><br /> <br /> <references/></div>

Dima Golovenko https://proteopedia.org/index.php?title=Sandbox_erice_4&diff=1092572 Sandbox erice 4 2010-06-09T12:38:37Z

<p>Dima Golovenko: /* Exploring the Structure */</p> <hr /> <div>'''Influenza neuraminidase''' is a glycoprotein in the influenza virus membrane. Before an infected cell can release the virus into its surroundings to infect new cells, neuraminidase must cleave sialic acid from both virus and cellular glycoproteins. Neuraminidase is a homotetramer -- here we will examine only one monomer.<br /> <br /> <br /> == Exploring the Structure ==<br /> <br /> <applet load='3cl0' size='300' frame='true' align='right' caption='Insert caption here' /><br /> <br /> Because of its important role in virus infectivity, several anti-viral drugs have been designed to target neuraminidase, including <scene name='Sandbox_erice_4/Zoom_3cl0/1'>oseltamavir</scene> (Tamiflu) and zanamivir (Relenza). Oseltamavir binding to neuraminidase moves glutamate 276 towards histidine 274, making more room for oseltamavir to bind tightly (PDB entry [[2hu4]]). But, in a common mutant (H274Y), a larger tyrosine replaces the smaller histidine 274, preventing glutamate 276 from moving to make room for oseltamavir binding, resulting in weaker drug binding and thus resistance (PDB entry [[3cl0]]). Luckily the H274Y neuraminidase mutant is still susceptible to zanamivir, which is smaller than oseltamavir.<br /> <ref>pmid:18480754</ref><br /> <br /> <scene name='Sandbox_erice_4/Scene_1/1'>TextToBeDisplayed</scene><br /> <br /> <scene name='Sandbox_erice_4/Common_mutants_2/1'>common mutant Y274</scene><br /> <br /> <references/><br /> <br /> [[Image:Example.jpg]]</div>

Dima Golovenko https://proteopedia.org/index.php?title=Sandbox_erice_4&diff=1092566 Sandbox erice 4 2010-06-09T12:32:12Z

<p>Dima Golovenko: </p> <hr /> <div>'''Influenza neuraminidase''' is a glycoprotein in the influenza virus membrane. Before an infected cell can release the virus into its surroundings to infect new cells, neuraminidase must cleave sialic acid from both virus and cellular glycoproteins. Neuraminidase is a homotetramer -- here we will examine only one monomer.<br /> <br /> <br /> == Exploring the Structure ==<br /> <br /> <applet load='3cl0' size='300' frame='true' align='right' caption='Insert caption here' /><br /> <br /> Because of its important role in virus infectivity, several anti-viral drugs have been designed to target neuraminidase, including <scene name='Sandbox_erice_4/Zoom_3cl0/1'>oseltamavir</scene> (Tamiflu) and zanamivir (Relenza). Oseltamavir binding to neuraminidase moves glutamate 276 towards histidine 274, making more room for oseltamavir to bind tightly (PDB entry [[2hu4]]). But, in a common mutant (H274Y), a larger tyrosine replaces the smaller histidine 274, preventing glutamate 276 from moving to make room for oseltamavir binding, resulting in weaker drug binding and thus resistance (PDB entry [[3cl0]]). Luckily the H274Y neuraminidase mutant is still susceptible to zanamivir, which is smaller than oseltamavir.<br /> <ref>pmid:18480754</ref><br /> <br /> <scene name='Sandbox_erice_4/Scene_1/1'>TextToBeDisplayed</scene><br /> <br /> <scene name='Sandbox_erice_4/Common_mutants_2/1'>common mutant Y274</scene><br /> <br /> <references/></div>

Dima Golovenko https://proteopedia.org/index.php?title=Sandbox_erice_4&diff=1092565 Sandbox erice 4 2010-06-09T12:31:15Z

<p>Dima Golovenko: </p> <hr /> <div>'''Influenza neuraminidase''' is a glycoprotein in the influenza virus membrane. Before an infected cell can release the virus into its surroundings to infect new cells, neuraminidase must cleave sialic acid from both virus and cellular glycoproteins. Neuraminidase is a homotetramer -- here we will examine only one monomer.<br /> <br /> <br /> == Exploring the Structure ==<br /> <br /> <applet load='3cl0' size='300' frame='true' align='right' caption='Insert caption here' /><br /> <br /> Because of its important role in virus infectivity, several anti-viral drugs have been designed to target neuraminidase, including <scene name='Sandbox_erice_4/Zoom_3cl0/1'>oseltamavir</scene> (Tamiflu) and zanamivir (Relenza). Oseltamavir binding to neuraminidase moves glutamate 276 towards histidine 274, making more room for oseltamavir to bind tightly (PDB entry [[2hu4]]). But, in a common mutant (H274Y), a larger tyrosine replaces the smaller histidine 274, preventing glutamate 276 from moving to make room for oseltamavir binding, resulting in weaker drug binding and thus resistance (PDB entry [[3cl0]]). Luckily the H274Y neuraminidase mutant is still susceptible to zanamivir, which is smaller than oseltamavir.<br /> <ref>pmid:18480754</ref><br /> <br /> <scene name='Sandbox_erice_4/Scene_1/1'>TextToBeDisplayed</scene><br /> <br /> <scene name='Sandbox_erice_4/Common_mutants_2/1'>TextToBeDisplayed</scene><br /> <br /> <references/></div>

Dima Golovenko https://proteopedia.org/index.php?title=Sandbox_erice_4&diff=1092563 Sandbox erice 4 2010-06-09T12:09:38Z

<p>Dima Golovenko: </p> <hr /> <div>'''Influenza neuraminidase''' is a glycoprotein in the influenza virus membrane. Before an infected cell can release the virus into its surroundings to infect new cells, neuraminidase must cleave sialic acid from both virus and cellular glycoproteins. Neuraminidase is a homotetramer -- here we will examine only one monomer.<br /> <br /> <br /> == Exploring the Structure ==<br /> <br /> <applet load='3cl0' size='300' frame='true' align='right' caption='Insert caption here' /><br /> <br /> Because of its important role in virus infectivity, several anti-viral drugs have been designed to target neuraminidase, including <scene name='Sandbox_erice_4/Zoom_3cl0/1'>oseltamavir</scene> (Tamiflu) and zanamivir (Relenza). Oseltamavir binding to neuraminidase moves glutamate 276 towards histidine 274, making more room for oseltamavir to bind tightly (PDB entry [[2hu4]]). But, in a common mutant (H274Y), a larger tyrosine replaces the smaller histidine 274, preventing glutamate 276 from moving to make room for oseltamavir binding, resulting in weaker drug binding and thus resistance (PDB entry [[3cl0]]). Luckily the H274Y neuraminidase mutant is still susceptible to zanamivir, which is smaller than oseltamavir.<br /> <ref>pmid:18480754</ref><br /> <br /> <scene name='Sandbox_erice_4/Scene_1/1'>TextToBeDisplayed</scene><br /> <br /> <references/></div>

Dima Golovenko https://proteopedia.org/index.php?title=Sandbox_erice_4&diff=1092559 Sandbox erice 4 2010-06-09T12:05:38Z

<p>Dima Golovenko: </p> <hr /> <div>'''Influenza neuraminidase''' is a glycoprotein in the influenza virus membrane. Before an infected cell can release the virus into its surroundings to infect new cells, neuraminidase must cleave sialic acid from both virus and cellular glycoproteins. Neuraminidase is a homotetramer -- here we will examine only one monomer.<br /> <br /> <br /> == Exploring the Structure ==<br /> <br /> <applet load='3cl0' size='300' frame='true' align='right' caption='Insert caption here' /><br /> <br /> Because of its important role in virus infectivity, several anti-viral drugs have been designed to target neuraminidase, including <scene name='Sandbox_erice_4/Zoom_3cl0/1'>oseltamavir</scene> (Tamiflu) and zanamivir (Relenza). Oseltamavir binding to neuraminidase moves glutamate 276 towards histidine 274, making more room for oseltamavir to bind tightly (PDB entry [[2hu4]]). But, in a common mutant (H274Y), a larger tyrosine replaces the smaller histidine 274, preventing glutamate 276 from moving to make room for oseltamavir binding, resulting in weaker drug binding and thus resistance (PDB entry [[3cl0]]). Luckily the H274Y neuraminidase mutant is still susceptible to zanamivir, which is smaller than oseltamavir.<br /> <ref>pmid:18480754</ref><br /> <br /> <references/></div>

Dima Golovenko https://proteopedia.org/index.php?title=Sandbox_erice_4&diff=1092555 Sandbox erice 4 2010-06-09T12:00:36Z

<p>Dima Golovenko: </p> <hr /> <div>[[Image:3cl0 4.png|thumb|left|150px|Influenza neuraminidase]]<br /> <br /> '''Influenza neuraminidase''' is a glycoprotein in the influenza virus membrane. Before an infected cell can release the virus into its surroundings to infect new cells, neuraminidase must cleave sialic acid from both virus and cellular glycoproteins. Neuraminidase is a homotetramer -- here we will examine only one monomer.<br /> <br /> <br /> == Exploring the Structure ==<br /> <br /> <applet load='3cl0' size='300' frame='true' align='right' caption='Insert caption here' /><br /> <br /> Because of its important role in virus infectivity, several anti-viral drugs have been designed to target neuraminidase, including <scene name='Sandbox_erice_4/Zoom_3cl0/1'>oseltamavir</scene> (Tamiflu) and zanamivir (Relenza). Oseltamavir binding to neuraminidase moves glutamate 276 towards histidine 274, making more room for oseltamavir to bind tightly (PDB entry [[2hu4]]). But, in a <scene name='Sandbox_erice_4/Tamiflu/1'>common mutant</scene> (H274Y), a larger tyrosine replaces the smaller histidine 274, preventing glutamate 276 from moving to make room for oseltamavir binding, resulting in weaker drug binding and thus resistance (PDB entry [[3cl0]]). Luckily the H274Y neuraminidase mutant is still susceptible to zanamivir, which is smaller than oseltamavir.<br /> <ref>pmid:18480754</ref><br /> <br /> <references/></div>

Dima Golovenko https://proteopedia.org/index.php?title=Sandbox_erice_4&diff=1092553 Sandbox erice 4 2010-06-09T11:59:48Z

<p>Dima Golovenko: </p> <hr /> <div>[[Image:3cl0 4.png|thumb|left|150px|Influenza neuraminidase]]<br /> <br /> '''Influenza neuraminidase''' is a glycoprotein in the influenza virus membrane. Before an infected cell can release the virus into its surroundings to infect new cells, neuraminidase must cleave sialic acid from both virus and cellular glycoproteins. Neuraminidase is a homotetramer -- here we will examine only one monomer.<br /> <br /> <br /> == Exploring the Structure ==<br /> <applet load='3cl0' size='300' frame='true' align='right' caption='Insert caption here' /><br /> <br /> Because of its important role in virus infectivity, several anti-viral drugs have been designed to target neuraminidase, including <scene name='Sandbox_erice_4/Zoom_3cl0/1'>oseltamavir</scene> (Tamiflu) and zanamivir (Relenza). Oseltamavir binding to neuraminidase moves glutamate 276 towards histidine 274, making more room for oseltamavir to bind tightly (PDB entry [[2hu4]]). But, in a <scene name='Sandbox_erice_4/Tamiflu/1'>common mutant</scene> (H274Y), a larger tyrosine replaces the smaller histidine 274, preventing glutamate 276 from moving to make room for oseltamavir binding, resulting in weaker drug binding and thus resistance (PDB entry [[3cl0]]). Luckily the H274Y neuraminidase mutant is still susceptible to zanamivir, which is smaller than oseltamavir.<br /> <ref>pmid:18480754</ref><br /> <br /> <references/></div>

Dima Golovenko https://proteopedia.org/index.php?title=Sandbox_erice_4&diff=1092550 Sandbox erice 4 2010-06-09T11:59:04Z

<p>Dima Golovenko: </p> <hr /> <div>[[Image:3cl0 4.png|thumb|left|150px|Influenza neuraminidase]]<br /> <br /> '''Influenza neuraminidase''' is a glycoprotein in the influenza virus membrane. Before an infected cell can release the virus into its surroundings to infect new cells, neuraminidase must cleave sialic acid from both virus and cellular glycoproteins. Neuraminidase is a homotetramer -- here we will examine only one monomer.<br /> <br /> <br /> == Exploring the Structure ==<br /> <applet load='3cl0' size='300' frame='true' align='right' caption='Insert caption here' /><br /> <br /> Because of its important role in virus infectivity, several anti-viral drugs have been designed to target neuraminidase, including <scene name='Sandbox_erice_4/Zoom_3cl0/1'>oseltamavir</scene> (Tamiflu) and zanamivir (Relenza). Oseltamavir binding to neuraminidase moves glutamate 276 towards histidine 274, making more room for oseltamavir to bind tightly (PDB entry [[2hu4]]). But, in a <scene name='Sandbox_erice_4/Tamiflu/1'>common mutant</scene> (H274Y), a larger tyrosine replaces the smaller histidine 274, preventing glutamate 276 from moving to make room for oseltamavir binding, resulting in weaker drug binding and thus resistance (PDB entry [[3cl0]]). Luckily the H274Y neuraminidase mutant is still susceptible to zanamivir, which is smaller than oseltamavir.<br /> <ref>pmid:18480754</ref><br /> <br /> <references/><br /> <br /> <applet load='3cl0' size='300' frame='true' align='right' caption='Insert caption here' /></div>

Dima Golovenko https://proteopedia.org/index.php?title=User:Dima_Golovenko/Sandbox_1&diff=1017063 User:Dima Golovenko/Sandbox 1 2009-11-16T12:13:26Z

<p>Dima Golovenko: testing keyword 'spacefill' from Jmol tutorial for the SCENE;</p> <hr /> <div>{{Seed}}<br /> [[Image:1ckq.png|left|200px]]<br /> <br /> <br /> {{STRUCTURE_1ckq| PDB=1ckq | SCENE= spacefill }} <br /> <br /> ===PRE-TRANSITION STATE ECO RI ENDONUCLEASE/COGNATE DNA (TCGCGAATTCGCG) COMPLEX===<br /> <br /> <br /> ==About this Structure==<br /> 1CKQ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CKQ OCA]. <br /> <br /> ==Reference==<br /> <br /> [[Category: Escherichia coli]]<br /> [[Category: Single protein]]<br /> [[Category: Horvath, M.]]<br /> [[Category: Rosenberg, J M.]]<br /> [[Category: Sequence-specific dna-protein complex]]<br /> [[Category: 6mA-sensitive endonuclease]]<br /> <br /> ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 20:52:50 2008''</div>

Dima Golovenko https://proteopedia.org/index.php?title=User:Dima_Golovenko/Sandbox_1&diff=1017062 User:Dima Golovenko/Sandbox 1 2009-11-16T11:31:57Z

<p>Dima Golovenko: New page: {{Seed}} 200px <br /> {{STRUCTURE_1ckq| PDB=1ckq | SCENE= }} <br /> <br /> ===PRE-TRANSITION STATE ECO RI ENDONUCLEASE/COGNATE DNA (TCGCGAATTCGCG) COMPLEX===<br /> <br /> <br /> ==About this Structure==<br /> 1CKQ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CKQ OCA]. <br /> <br /> ==Reference==<br /> <br /> [[Category: Escherichia coli]]<br /> [[Category: Single protein]]<br /> [[Category: Horvath, M.]]<br /> [[Category: Rosenberg, J M.]]<br /> [[Category: Sequence-specific dna-protein complex]]<br /> [[Category: 6mA-sensitive endonuclease]]<br /> <br /> ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 20:52:50 2008''</div>

Dima Golovenko https://proteopedia.org/index.php?title=Category:6mA-sensitive_endonuclease&diff=1015003 Category:6mA-sensitive endonuclease 2009-11-10T13:13:46Z

<p>Dima Golovenko: </p> <hr /> <div>List of 6-methyl adenine sensitive restriction endonucleases complexed with DNA. Position of modified by native methyltransferase adenine in a recognition site was experimentally determined.</div>

Dima Golovenko https://proteopedia.org/index.php?title=Category:6mA-sensitive_endonuclease&diff=1015001 Category:6mA-sensitive endonuclease 2009-11-10T13:11:55Z

<p>Dima Golovenko: </p> <hr /> <div>List of 6-methyl adenine sensitive restriction endonucleases complexed with DNA. Position of modified by native methyltransferase adenine in a recognition site is experimentally determined.</div>

Dima Golovenko https://proteopedia.org/index.php?title=Category:6mA-sensitive_endonuclease&diff=1014995 Category:6mA-sensitive endonuclease 2009-11-10T13:06:35Z

<p>Dima Golovenko: </p> <hr /> <div>List of 6-methyl adenine sensitive restriction endonucleases complexed with DNA. Position of modified cytosine in the recognition site is experimentally determined.<br /> <br /> To be included into the subcategory of REase-DNA crystal structures:<br /> 2e52<br /> 1kc6<br /> 1d02<br /> 1fok</div>

Dima Golovenko https://proteopedia.org/index.php?title=Category:6mA-sensitive_endonuclease&diff=1014986 Category:6mA-sensitive endonuclease 2009-11-10T12:50:50Z

<p>Dima Golovenko: need to be done.</p> <hr /> <div>To be included into the subcategory of REase-DNA crystal structures:<br /> 2e52<br /> 1kc6<br /> 1d02<br /> 1fok</div>

Dima Golovenko https://proteopedia.org/index.php?title=Category:6mA-sensitive_endonuclease&diff=1014985 Category:6mA-sensitive endonuclease 2009-11-10T12:48:30Z

<p>Dima Golovenko: PDB ID of 6mA-sensitive endonucleases crystal structures have been added;</p> <hr /> <div>2e52<br /> 1kc6<br /> 1d02<br /> 1fok</div>

Dima Golovenko https://proteopedia.org/index.php?title=User_talk:Eran_Hodis&diff=1014966 User talk:Eran Hodis 2009-11-10T12:23:49Z

<p>Dima Golovenko: /* Request for categories adding */</p> <hr /> <div>==News from Greece==<br /> Hi Eran,<br /> actually I was on vacation after the summer school of Erice! <br /> The last days I'm back in the lab and try to find the rythm of the experiments ;)<br /> I shown to my boss the proteopedia and my page..he is excited! Actually I'm writing a paper and I may use the proteopedia for making the pictures. I would like to ask you how can I export the pictures to my pc.<br /> We'll be in contact..you'll see the progress of my page!<br /> <br /> best wishes<br /> Maria<br /> ---------<br /> <br /> <br /> Hi Eran,<br /> Now back at home with access to my Mac. Much enjoyed meeting and talking with you. Carole and I enjoyed our round trip of Sicily, and we more or less walked our feet off in Pompei last Monday. Off to practice our golf swings now. I also talked to one of the head honchos of the Cambridge small molecule crystallographic database, and he was receptive to the idea of making a filterered subset of drugs and other biologically-active small molecules available to Proteopedia (read: ligands). If you are ever in the neighbourhood of Basel, look us up, and we can offer you a free place to sleep.<br /> best regards<br /> Trevor<br /> ---------<br /> <br /> Hi Eran. How are you? I'm Maria Ambrazi..do you remember from Erice? Can you send me your e-mail...I would like to ask you something on proteopedia!<br /> <br /> == Bad green link ==<br /> Eran,<br /> I have a green link which does not work, it should make a Ramachandran plot. When I attempt to edit it the SAT freezes and no other scenes can be loaded. In fact as I remember when I first made the scene the SAT froze. After the SAT freezes some of the links above and below this bad link no longer work. Is there a way that a developer can delete scenes?<br /> <br /> Karl<br /> <br /> ---------<br /> After I left the message for you, I decided to take a different approach and not use the link, but I would be interested in knowing what is wrong with the link if you can discover that. I named the link plot_tripep_disallowed.<br /> <br /> Karl<br /> <br /> <br /> == PDBsum site ==<br /> Eran,<br /> After exploring this site I have come to the conclusion that the entry page to this site changes from time to time. Is that correct? If so, I should give directions on the Ramachandran page how to generate the Ramachandran plot on PDBsum.<br /> <br /> By the way that site is a wonderful resource. I am going to include it in the computer resource exercise that I have my Biochemistry I students do.<br /> <br /> Karl<br /> <br /> Eran,<br /> I just realized that I was not thinking clearly this morning. I had forgotten that the url that I am using is coded for 1eve and Procheck, and therefore the site will open with the desired protein and information displayed.<br /> <br /> Karl<br /> <br /> == Proteopedia for teaching ==<br /> Hi Eran<br /> <br /> I'm in the middle of my labs using Proteopedia, and on balance I think it's a great improvement for this class - I run 6 streams of 60 students each in a 2nd year biochemistry class. Using sPDBv meant that they spent a lot of time struggling with the program, but proteopedia is letting them just think about the protein structure instead. So, overall positive. However, two things that have come up:<br /> <br /> 1) Secondary structure definitions - How does Jmol generate them? Are they user definable? Jmol is clearly using a different algorithm to sPDBv, so students are seeing inconsistency when they use both routes. (For the record, I agree with sPDBv's pick!)<br /> <br /> 2) More seriously, the display of backbone hydrogen bonds is wrong - not sure if this is something I'm doing wrong or a fault in Jmol. Backbone hydrogen bonds are being drawn between C-alphas rather than between carbonyl oxygens and peptide nitrogens. Check out the link at the very bottom of the page http://www.proteopedia.org/wiki/index.php/User:J._Shaun_Lott/BIOSCI_203 marked "What is wrong with this picture?" to see what I mean.<br /> <br /> cheers!<br /> <br /> Shaun<br /> <br /> == What to do with my students contributions ==<br /> <br /> Hi Eran,<br /> <br /> I am trying user talk to communicate instead of my email, since my question may be relevant to other educators. I have several student contributions that I wish to keep and others that ought to be erased eventually. I want to keep the good ones, and one bad one for illustration of a range of student abilities. I am not sure if its best to transfer the material to my page; start another page with student contributions, or to link to the student's pages. I have the passwords the student sites, so I can access the scripts. What do you suggest is best?<br /> <br /> Tom<br /> <br /> == Surfaces ==<br /> <br /> Hi Eran,<br /> <br /> I tried but could not figure out if a surface of one protomer could be colored differently from a surface of another protomer using the surface representation.<br /> <br /> Tom<br /> <br /> == more on surfaces ==<br /> <br /> Hi<br /> <br /> Surfaces are slow to load--such is life--but my experience is the same as yours. Only one color is available for the surfaces.<br/><br /> my best<br/><br /> Tom<br/><br /> PS. So, what is the Israeli greetings/salutation during Hannukah?<br /> <br /> == Cheers Eran! ==<br /> <br /> Thanks for the info. About the template text - it even appears here when I click the + tab in your talk page. I think it should be easy enough to limit the feature by namespace, as many WP extensions seem to be ns specific. <br /> <br /> <br /> BTW, did you ever consider installing something like 'liquid threads' to make discussion more 'fully featured'? I played with it on a small wiki, and it worked OK, but when you install it you loose all old discussions. For a while I wanted to merge something like PHP BB with WP to create a forum 'channel' for each page, which should be simple enough to do... --[[User:Dan Bolser|Dan Bolser]] 10:58, 5 January 2009 (IST)<br /> <br /> == RE: ==<br /> <br /> <br /> Agreed about the template text. I'll email/message you when we have it updated. As to liquid threads, we've never considered anything like that, although its clear that the current MediaWiki system of messages is less than intuitive to say the least. We'd be hesitant to make large changes whose stability is not guaranteed, but if you think this is something we should look into, please link me to the appropriate places where I can read more about it. Eran Hodis 13:59, 5 January 2009 (IST) <br /> <br /> : With respect to 'is [this] something we should look into', I'm not really sure. It depends on how much you want Proteopedia to function as a 'community discussion forum' in addition to being a 'community education portal'. Actually, something like 'technical community discussion' was the emphasis of PDBWiki, which is why we think that it stands distinct from Proteopedia (with its emphasis on education). So basically I think its up to you to look at what is possible and assess the potential benefit, which may be marginal. Liquid threads is at http://www.mediawiki.org/wiki/Extension:LiquidThreads However, as I said, I'd be more interested in seeing a mini 'PHP BB' appearing within each talk tab http://www.phpbb.com/ I don't know why there are no efforts to implement this (that I can find). Oh... I spoke to soon ;-D http://www.mediawikiusers.com/wiki/index.php/Projects:MediaWiki/phpBB_Integration but that seems a bit thin on details TBH... Anyway, I only mentioned this because you seem to have a good capacity to work on such features, and I think that such a feature would be generally useful to the wider wiki world. All the best --[[User:Dan Bolser|Dan Bolser]] 15:24, 5 January 2009 (IST)<br /> <br /> :: After poking around I found this, http://www.mediawiki.org/wiki/Extension:AWC's_Forum which looks very promising. --[[User:Dan Bolser|Dan Bolser]] 16:00, 5 January 2009 (IST)<br /> <br /> ==RE: Models==<br /> <br /> Thanks Eran! We have been busier than expected at the CBM (but what else is new). Still, we hope to continue working on Proteopedia to upload more and more images of models we have developed - as well as some working SMART Team pages. Joel let me know that all the models made it to him intact so he should have them to show off when he gets back on your side of the world. It is a pretty neat collection of a very interesting topic - so enjoy!<br /> <br /> -Mark<br /> <br /> == Moving scenes from one page to another ==<br /> <br /> Hi Eran,<br /> <br /> I am able to copy wiki script from one page and copy it to another page using copy command: I can do ths copy <nowiki><scene>...<scene/></nowiki> (assuming I wrote the syntax correctly) from User:Tom Gluick/Human Glutamine Synthetase (section) to User:Tom Gluick/Human Glutamine Synthetase (section)/quaternary a subpage. However, I would like to change the scene in the subpage, but when SAT is access in subpage, the scene is not found associated with the subpage. is there something that can be done to remedy this issue. It would certainly save me time if this were possible.<br /> <br /> Tom<br /> <br /> ==Other Media in Proteopedia?==<br /> <br /> Hi Eran,<br /> <br /> I have a question about the potential for additional media on pages. I know we can easily load and display images on Proteopedia, but is there any way to upload other file varieties - for example, simple flash animations (.swf) or something similar to that? Or, if we can't actually upload them to the Proteopedia webspace, is there any way to have files uploaded on our own server and just displayed on the proteopedia page - perhaps by using some html similar to the <img src="www.filename.jpg"> code you can use for linking to images)?<br /> <br /> -Mark<br /> <br /> ===tilman ===<br /> Eran, you are right. That page <br /> Http://proteopedia.org/wiki/index.php/User:Tilman_Schirmer/Sandbox_10<br /> is obsolete. I've saved the content to the proper Sandbox_10.<br /> <br /> You can delete it. Thanks,<br /> Tilman<br /> ==References==<br /> <br /> Thanks for the tip Eran. I seem to stumble across cool built in features for Proteopedia like that every time I use it! Keep up the good work.<br /> <br /> -Mark<br /> <br /> == good enough? ==<br /> <br /> Would you say, [[User:Ralf Stephan/Sandbox 2|this]] is good enough to replace [[2a7g]]? What more does it need for a page 'Thermolysin'? --[[User:Ralf Stephan|Ralf Stephan]] 16:57, 7 February 2009 (IST)<br /> <br /> :It's certainly enough to replace [[2a7g]], and a great start! (please do replace it) The automatically added abstract here doesn't seem to have anything to do with the structure. Is this indeed the primary publication for the structure? Some questions/comments about your additions: Consider making "metalloprotease" as a interwiki link. We have a not-so-well developed page on [[Matrix_metalloproteinases]], but none on metalloproteases, so the reader may wonder what is a metalloprotease and what is its enzymatic function. It says "calcium atoms (yellow)" but I don't see any calcium atoms in yellow, they are green for me (as they usually are by default). It's not made entirely clear what the HEXHH motif is, could you clarify? I feel the reader would also wonder why is it important to mention in the first sentence that the protein contains zinc and several calcium atoms. Also, what is the substrate usually? The green links look just spectacular, and I'm glad to see you've quickly gotten the hang of the Scene Authoring Tools. <br /> <br /> :A page called 'Thermolysin' is a great idea, are there any other structures? We could transclude a section from your new [[2a7g]] page as well as elaborate more -- especially if there are other structures. --[[User:Eran Hodis|Eran Hodis]] 02:34, 8 February 2009 (IST)<br /> ::*There are lots of other thermolysin structures, mostly inhibitors docking and soaked with different solvent concentrations (why these?).<br /> :::Just thinking that a topic page on thermolysin could use the other structures as well to present a fuller picture.<br /> ::*So, a topic has a set of structures, ideally of all structures, with the structures pointing to 'their' nearest topic?<br /> :::That's the current mode of thinking. Of course better ideas will be adopted.<br /> ::*Regarding yellow/green, that's an example of me unconsciously giving away personal genetic data ;) Really, if I have that problem, other R/G blind people would have, too, so I'd suggest a different color for calcium.<br /> :::Hmm, yes we actually were wondering if that would be a problem when we made the scene links green -- is it a problem? Unfortunately it would be quite unfeasible to change from green scene links at this point. As far as changing calcium to a color other than green -- green might be part of a big coloring scheme that we might want to stick with. We can have a discussion on this if need be. <br /> ::*/Wrt the paper, that paper is given by PDBsum, too, one of those where the protein is just an example in a technical presentation. I should have used a different one.<br /> :::Ok, in this case then it is probably acceptable to leave out the publication abstract. If we use a more fitting abstract, but one from authors that did not solve that structure, it might send the wrong impression to readers that the wrong set of authors solved the structure. If you choose to do this, I would make it clear that the abstract is not the official one for this structure, and list the authors that did solve the structure with the appropriate reference.<br /> ::*Yes, MMPs are only a small subset of metalloproteases and should link to that WP article, too. <br /> :::Ok good.<br /> ::Thanks also for the other hints. Is there a list of all structure pages that have been enhanced manually? I know there's a manually maintained list as part of the topic page list but I think there should be something automatical such that enhancements are not lost. --[[User:Ralf Stephan|Ralf Stephan]] 10:16, 8 February 2009 (IST)<br /> :::Agreed, but the way to do this has slipped my mind at the moment. Let's see if Jaime Prilusky knows and will respond on the mailing list. --[[User:Eran Hodis|Eran Hodis]] 12:27, 8 February 2009 (IST)<br /> <br /> == java.io.File not found ==<br /> <br /> Do you understand why the applet can't find the PDB file in [[Helix-turn-helix motif]]? --[[User:Ralf Stephan|Ralf Stephan]] 17:57, 8 February 2009 (IST)<br /> :Never mind, I found it out myself: I forgot to provide a scene. --[[User:Ralf Stephan|Ralf Stephan]] 18:14, 8 February 2009 (IST)<br /> <br /> ==Image Issue==<br /> Hi Eran, <br /> I got your message and will take care of it. I think modified images were okay. <br /> Thanks!<br /> Leah<br /> <br /> ditto leah. thanks! becca<br /> <br /> ==Scrambled Eggs ==<br /> Any chance you are referring to egg cells and fertilization ? :)<br /> == Applet Behavior ==<br /> <br /> Eran, the applets in Z-DNA page seem to be behaving erratically. At times there <br /> is no display and at times they are not in the frame. There is also a problem<br /> with the sugar puckering option in DNA page. The applet freezes when this is selected.<br /> Could you please verify if you are facing the same problems?<br /> <br /> [[User:Adithya Sagar|Adithya Sagar]] 21:06, 22 October 2009 (IST)<br /> <br /> ==Image license==<br /> <br /> Originally from {Molecular cell biology. Lodish, Harvey 5 ed: - New York : W. H. Freeman and Co., 2003, 973 s. b ill. ISBN: 0-7167-4366-3. Libris: 8926100.}<br /> <br /> Original uploader was Roadnottaken at en.wikipedia 2007-03-22<br /> <br /> The image was found from Wikipedia and was a modified image that is a "GNU Free Documentation License"<br /> I changed the properties of my image file and it should give the proper acknowledgments.<br /> <br /> -Matt<br /> <br /> ==Restriction endonucleases complexes with DNA - PspGI (3bm3) case==<br /> <br /> Hi, Eran!<br /> <br /> It is nice to see such quick assistance with tech bug.<br /> It is pity I found proteopedia after we published article on two protein-DNA structures.<br /> I will try in my Ph.D. thesis to visualise review of REase-DNA complexes with proteopedia.<br /> <br /> greatings from Vilne,<br /> Dima<br /> <br /> Now I see it was not bug but database case.<br /> <br /> ==molscript2Jmol==<br /> <br /> Hi,<br /> <br /> Is it possible simple coversion or implementation of molscript input and/or .mols files to Jmol script?<br /> <br /> ==Request for categories adding==<br /> <br /> Could I add in "Categories" chapter my own specific markups? For example, I would like to classify restriction endonucleases complexes with DNA in respect of what native methyltranferases are: 6-methyl adenine, 5- or 4- methyl cytosine?<br /> <br /> Dima</div>

Dima Golovenko https://proteopedia.org/index.php?title=User_talk:Eran_Hodis&diff=1014965 User talk:Eran Hodis 2009-11-10T12:23:11Z

<p>Dima Golovenko: /* Request for categories adding */</p> <hr /> <div>==News from Greece==<br /> Hi Eran,<br /> actually I was on vacation after the summer school of Erice! <br /> The last days I'm back in the lab and try to find the rythm of the experiments ;)<br /> I shown to my boss the proteopedia and my page..he is excited! Actually I'm writing a paper and I may use the proteopedia for making the pictures. I would like to ask you how can I export the pictures to my pc.<br /> We'll be in contact..you'll see the progress of my page!<br /> <br /> best wishes<br /> Maria<br /> ---------<br /> <br /> <br /> Hi Eran,<br /> Now back at home with access to my Mac. Much enjoyed meeting and talking with you. Carole and I enjoyed our round trip of Sicily, and we more or less walked our feet off in Pompei last Monday. Off to practice our golf swings now. I also talked to one of the head honchos of the Cambridge small molecule crystallographic database, and he was receptive to the idea of making a filterered subset of drugs and other biologically-active small molecules available to Proteopedia (read: ligands). If you are ever in the neighbourhood of Basel, look us up, and we can offer you a free place to sleep.<br /> best regards<br /> Trevor<br /> ---------<br /> <br /> Hi Eran. How are you? I'm Maria Ambrazi..do you remember from Erice? Can you send me your e-mail...I would like to ask you something on proteopedia!<br /> <br /> == Bad green link ==<br /> Eran,<br /> I have a green link which does not work, it should make a Ramachandran plot. When I attempt to edit it the SAT freezes and no other scenes can be loaded. In fact as I remember when I first made the scene the SAT froze. After the SAT freezes some of the links above and below this bad link no longer work. Is there a way that a developer can delete scenes?<br /> <br /> Karl<br /> <br /> ---------<br /> After I left the message for you, I decided to take a different approach and not use the link, but I would be interested in knowing what is wrong with the link if you can discover that. I named the link plot_tripep_disallowed.<br /> <br /> Karl<br /> <br /> <br /> == PDBsum site ==<br /> Eran,<br /> After exploring this site I have come to the conclusion that the entry page to this site changes from time to time. Is that correct? If so, I should give directions on the Ramachandran page how to generate the Ramachandran plot on PDBsum.<br /> <br /> By the way that site is a wonderful resource. I am going to include it in the computer resource exercise that I have my Biochemistry I students do.<br /> <br /> Karl<br /> <br /> Eran,<br /> I just realized that I was not thinking clearly this morning. I had forgotten that the url that I am using is coded for 1eve and Procheck, and therefore the site will open with the desired protein and information displayed.<br /> <br /> Karl<br /> <br /> == Proteopedia for teaching ==<br /> Hi Eran<br /> <br /> I'm in the middle of my labs using Proteopedia, and on balance I think it's a great improvement for this class - I run 6 streams of 60 students each in a 2nd year biochemistry class. Using sPDBv meant that they spent a lot of time struggling with the program, but proteopedia is letting them just think about the protein structure instead. So, overall positive. However, two things that have come up:<br /> <br /> 1) Secondary structure definitions - How does Jmol generate them? Are they user definable? Jmol is clearly using a different algorithm to sPDBv, so students are seeing inconsistency when they use both routes. (For the record, I agree with sPDBv's pick!)<br /> <br /> 2) More seriously, the display of backbone hydrogen bonds is wrong - not sure if this is something I'm doing wrong or a fault in Jmol. Backbone hydrogen bonds are being drawn between C-alphas rather than between carbonyl oxygens and peptide nitrogens. Check out the link at the very bottom of the page http://www.proteopedia.org/wiki/index.php/User:J._Shaun_Lott/BIOSCI_203 marked "What is wrong with this picture?" to see what I mean.<br /> <br /> cheers!<br /> <br /> Shaun<br /> <br /> == What to do with my students contributions ==<br /> <br /> Hi Eran,<br /> <br /> I am trying user talk to communicate instead of my email, since my question may be relevant to other educators. I have several student contributions that I wish to keep and others that ought to be erased eventually. I want to keep the good ones, and one bad one for illustration of a range of student abilities. I am not sure if its best to transfer the material to my page; start another page with student contributions, or to link to the student's pages. I have the passwords the student sites, so I can access the scripts. What do you suggest is best?<br /> <br /> Tom<br /> <br /> == Surfaces ==<br /> <br /> Hi Eran,<br /> <br /> I tried but could not figure out if a surface of one protomer could be colored differently from a surface of another protomer using the surface representation.<br /> <br /> Tom<br /> <br /> == more on surfaces ==<br /> <br /> Hi<br /> <br /> Surfaces are slow to load--such is life--but my experience is the same as yours. Only one color is available for the surfaces.<br/><br /> my best<br/><br /> Tom<br/><br /> PS. So, what is the Israeli greetings/salutation during Hannukah?<br /> <br /> == Cheers Eran! ==<br /> <br /> Thanks for the info. About the template text - it even appears here when I click the + tab in your talk page. I think it should be easy enough to limit the feature by namespace, as many WP extensions seem to be ns specific. <br /> <br /> <br /> BTW, did you ever consider installing something like 'liquid threads' to make discussion more 'fully featured'? I played with it on a small wiki, and it worked OK, but when you install it you loose all old discussions. For a while I wanted to merge something like PHP BB with WP to create a forum 'channel' for each page, which should be simple enough to do... --[[User:Dan Bolser|Dan Bolser]] 10:58, 5 January 2009 (IST)<br /> <br /> == RE: ==<br /> <br /> <br /> Agreed about the template text. I'll email/message you when we have it updated. As to liquid threads, we've never considered anything like that, although its clear that the current MediaWiki system of messages is less than intuitive to say the least. We'd be hesitant to make large changes whose stability is not guaranteed, but if you think this is something we should look into, please link me to the appropriate places where I can read more about it. Eran Hodis 13:59, 5 January 2009 (IST) <br /> <br /> : With respect to 'is [this] something we should look into', I'm not really sure. It depends on how much you want Proteopedia to function as a 'community discussion forum' in addition to being a 'community education portal'. Actually, something like 'technical community discussion' was the emphasis of PDBWiki, which is why we think that it stands distinct from Proteopedia (with its emphasis on education). So basically I think its up to you to look at what is possible and assess the potential benefit, which may be marginal. Liquid threads is at http://www.mediawiki.org/wiki/Extension:LiquidThreads However, as I said, I'd be more interested in seeing a mini 'PHP BB' appearing within each talk tab http://www.phpbb.com/ I don't know why there are no efforts to implement this (that I can find). Oh... I spoke to soon ;-D http://www.mediawikiusers.com/wiki/index.php/Projects:MediaWiki/phpBB_Integration but that seems a bit thin on details TBH... Anyway, I only mentioned this because you seem to have a good capacity to work on such features, and I think that such a feature would be generally useful to the wider wiki world. All the best --[[User:Dan Bolser|Dan Bolser]] 15:24, 5 January 2009 (IST)<br /> <br /> :: After poking around I found this, http://www.mediawiki.org/wiki/Extension:AWC's_Forum which looks very promising. --[[User:Dan Bolser|Dan Bolser]] 16:00, 5 January 2009 (IST)<br /> <br /> ==RE: Models==<br /> <br /> Thanks Eran! We have been busier than expected at the CBM (but what else is new). Still, we hope to continue working on Proteopedia to upload more and more images of models we have developed - as well as some working SMART Team pages. Joel let me know that all the models made it to him intact so he should have them to show off when he gets back on your side of the world. It is a pretty neat collection of a very interesting topic - so enjoy!<br /> <br /> -Mark<br /> <br /> == Moving scenes from one page to another ==<br /> <br /> Hi Eran,<br /> <br /> I am able to copy wiki script from one page and copy it to another page using copy command: I can do ths copy <nowiki><scene>...<scene/></nowiki> (assuming I wrote the syntax correctly) from User:Tom Gluick/Human Glutamine Synthetase (section) to User:Tom Gluick/Human Glutamine Synthetase (section)/quaternary a subpage. However, I would like to change the scene in the subpage, but when SAT is access in subpage, the scene is not found associated with the subpage. is there something that can be done to remedy this issue. It would certainly save me time if this were possible.<br /> <br /> Tom<br /> <br /> ==Other Media in Proteopedia?==<br /> <br /> Hi Eran,<br /> <br /> I have a question about the potential for additional media on pages. I know we can easily load and display images on Proteopedia, but is there any way to upload other file varieties - for example, simple flash animations (.swf) or something similar to that? Or, if we can't actually upload them to the Proteopedia webspace, is there any way to have files uploaded on our own server and just displayed on the proteopedia page - perhaps by using some html similar to the <img src="www.filename.jpg"> code you can use for linking to images)?<br /> <br /> -Mark<br /> <br /> ===tilman ===<br /> Eran, you are right. That page <br /> Http://proteopedia.org/wiki/index.php/User:Tilman_Schirmer/Sandbox_10<br /> is obsolete. I've saved the content to the proper Sandbox_10.<br /> <br /> You can delete it. Thanks,<br /> Tilman<br /> ==References==<br /> <br /> Thanks for the tip Eran. I seem to stumble across cool built in features for Proteopedia like that every time I use it! Keep up the good work.<br /> <br /> -Mark<br /> <br /> == good enough? ==<br /> <br /> Would you say, [[User:Ralf Stephan/Sandbox 2|this]] is good enough to replace [[2a7g]]? What more does it need for a page 'Thermolysin'? --[[User:Ralf Stephan|Ralf Stephan]] 16:57, 7 February 2009 (IST)<br /> <br /> :It's certainly enough to replace [[2a7g]], and a great start! (please do replace it) The automatically added abstract here doesn't seem to have anything to do with the structure. Is this indeed the primary publication for the structure? Some questions/comments about your additions: Consider making "metalloprotease" as a interwiki link. We have a not-so-well developed page on [[Matrix_metalloproteinases]], but none on metalloproteases, so the reader may wonder what is a metalloprotease and what is its enzymatic function. It says "calcium atoms (yellow)" but I don't see any calcium atoms in yellow, they are green for me (as they usually are by default). It's not made entirely clear what the HEXHH motif is, could you clarify? I feel the reader would also wonder why is it important to mention in the first sentence that the protein contains zinc and several calcium atoms. Also, what is the substrate usually? The green links look just spectacular, and I'm glad to see you've quickly gotten the hang of the Scene Authoring Tools. <br /> <br /> :A page called 'Thermolysin' is a great idea, are there any other structures? We could transclude a section from your new [[2a7g]] page as well as elaborate more -- especially if there are other structures. --[[User:Eran Hodis|Eran Hodis]] 02:34, 8 February 2009 (IST)<br /> ::*There are lots of other thermolysin structures, mostly inhibitors docking and soaked with different solvent concentrations (why these?).<br /> :::Just thinking that a topic page on thermolysin could use the other structures as well to present a fuller picture.<br /> ::*So, a topic has a set of structures, ideally of all structures, with the structures pointing to 'their' nearest topic?<br /> :::That's the current mode of thinking. Of course better ideas will be adopted.<br /> ::*Regarding yellow/green, that's an example of me unconsciously giving away personal genetic data ;) Really, if I have that problem, other R/G blind people would have, too, so I'd suggest a different color for calcium.<br /> :::Hmm, yes we actually were wondering if that would be a problem when we made the scene links green -- is it a problem? Unfortunately it would be quite unfeasible to change from green scene links at this point. As far as changing calcium to a color other than green -- green might be part of a big coloring scheme that we might want to stick with. We can have a discussion on this if need be. <br /> ::*/Wrt the paper, that paper is given by PDBsum, too, one of those where the protein is just an example in a technical presentation. I should have used a different one.<br /> :::Ok, in this case then it is probably acceptable to leave out the publication abstract. If we use a more fitting abstract, but one from authors that did not solve that structure, it might send the wrong impression to readers that the wrong set of authors solved the structure. If you choose to do this, I would make it clear that the abstract is not the official one for this structure, and list the authors that did solve the structure with the appropriate reference.<br /> ::*Yes, MMPs are only a small subset of metalloproteases and should link to that WP article, too. <br /> :::Ok good.<br /> ::Thanks also for the other hints. Is there a list of all structure pages that have been enhanced manually? I know there's a manually maintained list as part of the topic page list but I think there should be something automatical such that enhancements are not lost. --[[User:Ralf Stephan|Ralf Stephan]] 10:16, 8 February 2009 (IST)<br /> :::Agreed, but the way to do this has slipped my mind at the moment. Let's see if Jaime Prilusky knows and will respond on the mailing list. --[[User:Eran Hodis|Eran Hodis]] 12:27, 8 February 2009 (IST)<br /> <br /> == java.io.File not found ==<br /> <br /> Do you understand why the applet can't find the PDB file in [[Helix-turn-helix motif]]? --[[User:Ralf Stephan|Ralf Stephan]] 17:57, 8 February 2009 (IST)<br /> :Never mind, I found it out myself: I forgot to provide a scene. --[[User:Ralf Stephan|Ralf Stephan]] 18:14, 8 February 2009 (IST)<br /> <br /> ==Image Issue==<br /> Hi Eran, <br /> I got your message and will take care of it. I think modified images were okay. <br /> Thanks!<br /> Leah<br /> <br /> ditto leah. thanks! becca<br /> <br /> ==Scrambled Eggs ==<br /> Any chance you are referring to egg cells and fertilization ? :)<br /> == Applet Behavior ==<br /> <br /> Eran, the applets in Z-DNA page seem to be behaving erratically. At times there <br /> is no display and at times they are not in the frame. There is also a problem<br /> with the sugar puckering option in DNA page. The applet freezes when this is selected.<br /> Could you please verify if you are facing the same problems?<br /> <br /> [[User:Adithya Sagar|Adithya Sagar]] 21:06, 22 October 2009 (IST)<br /> <br /> ==Image license==<br /> <br /> Originally from {Molecular cell biology. Lodish, Harvey 5 ed: - New York : W. H. Freeman and Co., 2003, 973 s. b ill. ISBN: 0-7167-4366-3. Libris: 8926100.}<br /> <br /> Original uploader was Roadnottaken at en.wikipedia 2007-03-22<br /> <br /> The image was found from Wikipedia and was a modified image that is a "GNU Free Documentation License"<br /> I changed the properties of my image file and it should give the proper acknowledgments.<br /> <br /> -Matt<br /> <br /> ==Restriction endonucleases complexes with DNA - PspGI (3bm3) case==<br /> <br /> Hi, Eran!<br /> <br /> It is nice to see such quick assistance with tech bug.<br /> It is pity I found proteopedia after we published article on two protein-DNA structures.<br /> I will try in my Ph.D. thesis to visualise review of REase-DNA complexes with proteopedia.<br /> <br /> greatings from Vilne,<br /> Dima<br /> <br /> Now I see it was not bug but database case.<br /> <br /> ==molscript2Jmol==<br /> <br /> Hi,<br /> <br /> Is it possible simple coversion or implementation of molscript input and/or .mols files to Jmol script?<br /> <br /> ==Request for categories adding==<br /> <br /> Could I add in "Categories" chapter my own specific markups? For example, I would like to classify restriction endonucleases complexes with DNA in respect of what native methyltranferases are: 6-methyl adenine, 5- or 4- methyl citosine?<br /> <br /> Dima</div>

Dima Golovenko https://proteopedia.org/index.php?title=User_talk:Eran_Hodis&diff=1014905 User talk:Eran Hodis 2009-11-10T07:44:05Z

<p>Dima Golovenko: /* molscript2Jmol */</p> <hr /> <div>==News from Greece==<br /> Hi Eran,<br /> actually I was on vacation after the summer school of Erice! <br /> The last days I'm back in the lab and try to find the rythm of the experiments ;)<br /> I shown to my boss the proteopedia and my page..he is excited! Actually I'm writing a paper and I may use the proteopedia for making the pictures. I would like to ask you how can I export the pictures to my pc.<br /> We'll be in contact..you'll see the progress of my page!<br /> <br /> best wishes<br /> Maria<br /> ---------<br /> <br /> <br /> Hi Eran,<br /> Now back at home with access to my Mac. Much enjoyed meeting and talking with you. Carole and I enjoyed our round trip of Sicily, and we more or less walked our feet off in Pompei last Monday. Off to practice our golf swings now. I also talked to one of the head honchos of the Cambridge small molecule crystallographic database, and he was receptive to the idea of making a filterered subset of drugs and other biologically-active small molecules available to Proteopedia (read: ligands). If you are ever in the neighbourhood of Basel, look us up, and we can offer you a free place to sleep.<br /> best regards<br /> Trevor<br /> ---------<br /> <br /> Hi Eran. How are you? I'm Maria Ambrazi..do you remember from Erice? Can you send me your e-mail...I would like to ask you something on proteopedia!<br /> <br /> == Bad green link ==<br /> Eran,<br /> I have a green link which does not work, it should make a Ramachandran plot. When I attempt to edit it the SAT freezes and no other scenes can be loaded. In fact as I remember when I first made the scene the SAT froze. After the SAT freezes some of the links above and below this bad link no longer work. Is there a way that a developer can delete scenes?<br /> <br /> Karl<br /> <br /> ---------<br /> After I left the message for you, I decided to take a different approach and not use the link, but I would be interested in knowing what is wrong with the link if you can discover that. I named the link plot_tripep_disallowed.<br /> <br /> Karl<br /> <br /> <br /> == PDBsum site ==<br /> Eran,<br /> After exploring this site I have come to the conclusion that the entry page to this site changes from time to time. Is that correct? If so, I should give directions on the Ramachandran page how to generate the Ramachandran plot on PDBsum.<br /> <br /> By the way that site is a wonderful resource. I am going to include it in the computer resource exercise that I have my Biochemistry I students do.<br /> <br /> Karl<br /> <br /> Eran,<br /> I just realized that I was not thinking clearly this morning. I had forgotten that the url that I am using is coded for 1eve and Procheck, and therefore the site will open with the desired protein and information displayed.<br /> <br /> Karl<br /> <br /> == Proteopedia for teaching ==<br /> Hi Eran<br /> <br /> I'm in the middle of my labs using Proteopedia, and on balance I think it's a great improvement for this class - I run 6 streams of 60 students each in a 2nd year biochemistry class. Using sPDBv meant that they spent a lot of time struggling with the program, but proteopedia is letting them just think about the protein structure instead. So, overall positive. However, two things that have come up:<br /> <br /> 1) Secondary structure definitions - How does Jmol generate them? Are they user definable? Jmol is clearly using a different algorithm to sPDBv, so students are seeing inconsistency when they use both routes. (For the record, I agree with sPDBv's pick!)<br /> <br /> 2) More seriously, the display of backbone hydrogen bonds is wrong - not sure if this is something I'm doing wrong or a fault in Jmol. Backbone hydrogen bonds are being drawn between C-alphas rather than between carbonyl oxygens and peptide nitrogens. Check out the link at the very bottom of the page http://www.proteopedia.org/wiki/index.php/User:J._Shaun_Lott/BIOSCI_203 marked "What is wrong with this picture?" to see what I mean.<br /> <br /> cheers!<br /> <br /> Shaun<br /> <br /> == What to do with my students contributions ==<br /> <br /> Hi Eran,<br /> <br /> I am trying user talk to communicate instead of my email, since my question may be relevant to other educators. I have several student contributions that I wish to keep and others that ought to be erased eventually. I want to keep the good ones, and one bad one for illustration of a range of student abilities. I am not sure if its best to transfer the material to my page; start another page with student contributions, or to link to the student's pages. I have the passwords the student sites, so I can access the scripts. What do you suggest is best?<br /> <br /> Tom<br /> <br /> == Surfaces ==<br /> <br /> Hi Eran,<br /> <br /> I tried but could not figure out if a surface of one protomer could be colored differently from a surface of another protomer using the surface representation.<br /> <br /> Tom<br /> <br /> == more on surfaces ==<br /> <br /> Hi<br /> <br /> Surfaces are slow to load--such is life--but my experience is the same as yours. Only one color is available for the surfaces.<br/><br /> my best<br/><br /> Tom<br/><br /> PS. So, what is the Israeli greetings/salutation during Hannukah?<br /> <br /> == Cheers Eran! ==<br /> <br /> Thanks for the info. About the template text - it even appears here when I click the + tab in your talk page. I think it should be easy enough to limit the feature by namespace, as many WP extensions seem to be ns specific. <br /> <br /> <br /> BTW, did you ever consider installing something like 'liquid threads' to make discussion more 'fully featured'? I played with it on a small wiki, and it worked OK, but when you install it you loose all old discussions. For a while I wanted to merge something like PHP BB with WP to create a forum 'channel' for each page, which should be simple enough to do... --[[User:Dan Bolser|Dan Bolser]] 10:58, 5 January 2009 (IST)<br /> <br /> == RE: ==<br /> <br /> <br /> Agreed about the template text. I'll email/message you when we have it updated. As to liquid threads, we've never considered anything like that, although its clear that the current MediaWiki system of messages is less than intuitive to say the least. We'd be hesitant to make large changes whose stability is not guaranteed, but if you think this is something we should look into, please link me to the appropriate places where I can read more about it. Eran Hodis 13:59, 5 January 2009 (IST) <br /> <br /> : With respect to 'is [this] something we should look into', I'm not really sure. It depends on how much you want Proteopedia to function as a 'community discussion forum' in addition to being a 'community education portal'. Actually, something like 'technical community discussion' was the emphasis of PDBWiki, which is why we think that it stands distinct from Proteopedia (with its emphasis on education). So basically I think its up to you to look at what is possible and assess the potential benefit, which may be marginal. Liquid threads is at http://www.mediawiki.org/wiki/Extension:LiquidThreads However, as I said, I'd be more interested in seeing a mini 'PHP BB' appearing within each talk tab http://www.phpbb.com/ I don't know why there are no efforts to implement this (that I can find). Oh... I spoke to soon ;-D http://www.mediawikiusers.com/wiki/index.php/Projects:MediaWiki/phpBB_Integration but that seems a bit thin on details TBH... Anyway, I only mentioned this because you seem to have a good capacity to work on such features, and I think that such a feature would be generally useful to the wider wiki world. All the best --[[User:Dan Bolser|Dan Bolser]] 15:24, 5 January 2009 (IST)<br /> <br /> :: After poking around I found this, http://www.mediawiki.org/wiki/Extension:AWC's_Forum which looks very promising. --[[User:Dan Bolser|Dan Bolser]] 16:00, 5 January 2009 (IST)<br /> <br /> ==RE: Models==<br /> <br /> Thanks Eran! We have been busier than expected at the CBM (but what else is new). Still, we hope to continue working on Proteopedia to upload more and more images of models we have developed - as well as some working SMART Team pages. Joel let me know that all the models made it to him intact so he should have them to show off when he gets back on your side of the world. It is a pretty neat collection of a very interesting topic - so enjoy!<br /> <br /> -Mark<br /> <br /> == Moving scenes from one page to another ==<br /> <br /> Hi Eran,<br /> <br /> I am able to copy wiki script from one page and copy it to another page using copy command: I can do ths copy <nowiki><scene>...<scene/></nowiki> (assuming I wrote the syntax correctly) from User:Tom Gluick/Human Glutamine Synthetase (section) to User:Tom Gluick/Human Glutamine Synthetase (section)/quaternary a subpage. However, I would like to change the scene in the subpage, but when SAT is access in subpage, the scene is not found associated with the subpage. is there something that can be done to remedy this issue. It would certainly save me time if this were possible.<br /> <br /> Tom<br /> <br /> ==Other Media in Proteopedia?==<br /> <br /> Hi Eran,<br /> <br /> I have a question about the potential for additional media on pages. I know we can easily load and display images on Proteopedia, but is there any way to upload other file varieties - for example, simple flash animations (.swf) or something similar to that? Or, if we can't actually upload them to the Proteopedia webspace, is there any way to have files uploaded on our own server and just displayed on the proteopedia page - perhaps by using some html similar to the <img src="www.filename.jpg"> code you can use for linking to images)?<br /> <br /> -Mark<br /> <br /> ===tilman ===<br /> Eran, you are right. That page <br /> Http://proteopedia.org/wiki/index.php/User:Tilman_Schirmer/Sandbox_10<br /> is obsolete. I've saved the content to the proper Sandbox_10.<br /> <br /> You can delete it. Thanks,<br /> Tilman<br /> ==References==<br /> <br /> Thanks for the tip Eran. I seem to stumble across cool built in features for Proteopedia like that every time I use it! Keep up the good work.<br /> <br /> -Mark<br /> <br /> == good enough? ==<br /> <br /> Would you say, [[User:Ralf Stephan/Sandbox 2|this]] is good enough to replace [[2a7g]]? What more does it need for a page 'Thermolysin'? --[[User:Ralf Stephan|Ralf Stephan]] 16:57, 7 February 2009 (IST)<br /> <br /> :It's certainly enough to replace [[2a7g]], and a great start! (please do replace it) The automatically added abstract here doesn't seem to have anything to do with the structure. Is this indeed the primary publication for the structure? Some questions/comments about your additions: Consider making "metalloprotease" as a interwiki link. We have a not-so-well developed page on [[Matrix_metalloproteinases]], but none on metalloproteases, so the reader may wonder what is a metalloprotease and what is its enzymatic function. It says "calcium atoms (yellow)" but I don't see any calcium atoms in yellow, they are green for me (as they usually are by default). It's not made entirely clear what the HEXHH motif is, could you clarify? I feel the reader would also wonder why is it important to mention in the first sentence that the protein contains zinc and several calcium atoms. Also, what is the substrate usually? The green links look just spectacular, and I'm glad to see you've quickly gotten the hang of the Scene Authoring Tools. <br /> <br /> :A page called 'Thermolysin' is a great idea, are there any other structures? We could transclude a section from your new [[2a7g]] page as well as elaborate more -- especially if there are other structures. --[[User:Eran Hodis|Eran Hodis]] 02:34, 8 February 2009 (IST)<br /> ::*There are lots of other thermolysin structures, mostly inhibitors docking and soaked with different solvent concentrations (why these?).<br /> :::Just thinking that a topic page on thermolysin could use the other structures as well to present a fuller picture.<br /> ::*So, a topic has a set of structures, ideally of all structures, with the structures pointing to 'their' nearest topic?<br /> :::That's the current mode of thinking. Of course better ideas will be adopted.<br /> ::*Regarding yellow/green, that's an example of me unconsciously giving away personal genetic data ;) Really, if I have that problem, other R/G blind people would have, too, so I'd suggest a different color for calcium.<br /> :::Hmm, yes we actually were wondering if that would be a problem when we made the scene links green -- is it a problem? Unfortunately it would be quite unfeasible to change from green scene links at this point. As far as changing calcium to a color other than green -- green might be part of a big coloring scheme that we might want to stick with. We can have a discussion on this if need be. <br /> ::*/Wrt the paper, that paper is given by PDBsum, too, one of those where the protein is just an example in a technical presentation. I should have used a different one.<br /> :::Ok, in this case then it is probably acceptable to leave out the publication abstract. If we use a more fitting abstract, but one from authors that did not solve that structure, it might send the wrong impression to readers that the wrong set of authors solved the structure. If you choose to do this, I would make it clear that the abstract is not the official one for this structure, and list the authors that did solve the structure with the appropriate reference.<br /> ::*Yes, MMPs are only a small subset of metalloproteases and should link to that WP article, too. <br /> :::Ok good.<br /> ::Thanks also for the other hints. Is there a list of all structure pages that have been enhanced manually? I know there's a manually maintained list as part of the topic page list but I think there should be something automatical such that enhancements are not lost. --[[User:Ralf Stephan|Ralf Stephan]] 10:16, 8 February 2009 (IST)<br /> :::Agreed, but the way to do this has slipped my mind at the moment. Let's see if Jaime Prilusky knows and will respond on the mailing list. --[[User:Eran Hodis|Eran Hodis]] 12:27, 8 February 2009 (IST)<br /> <br /> == java.io.File not found ==<br /> <br /> Do you understand why the applet can't find the PDB file in [[Helix-turn-helix motif]]? --[[User:Ralf Stephan|Ralf Stephan]] 17:57, 8 February 2009 (IST)<br /> :Never mind, I found it out myself: I forgot to provide a scene. --[[User:Ralf Stephan|Ralf Stephan]] 18:14, 8 February 2009 (IST)<br /> <br /> ==Image Issue==<br /> Hi Eran, <br /> I got your message and will take care of it. I think modified images were okay. <br /> Thanks!<br /> Leah<br /> <br /> ditto leah. thanks! becca<br /> <br /> ==Scrambled Eggs ==<br /> Any chance you are referring to egg cells and fertilization ? :)<br /> == Applet Behavior ==<br /> <br /> Eran, the applets in Z-DNA page seem to be behaving erratically. At times there <br /> is no display and at times they are not in the frame. There is also a problem<br /> with the sugar puckering option in DNA page. The applet freezes when this is selected.<br /> Could you please verify if you are facing the same problems?<br /> <br /> [[User:Adithya Sagar|Adithya Sagar]] 21:06, 22 October 2009 (IST)<br /> <br /> ==Image license==<br /> <br /> Originally from {Molecular cell biology. Lodish, Harvey 5 ed: - New York : W. H. Freeman and Co., 2003, 973 s. b ill. ISBN: 0-7167-4366-3. Libris: 8926100.}<br /> <br /> Original uploader was Roadnottaken at en.wikipedia 2007-03-22<br /> <br /> The image was found from Wikipedia and was a modified image that is a "GNU Free Documentation License"<br /> I changed the properties of my image file and it should give the proper acknowledgments.<br /> <br /> -Matt<br /> <br /> ==Restriction endonucleases complexes with DNA - PspGI (3bm3) case==<br /> <br /> Hi, Eran!<br /> <br /> It is nice to see such quick assistance with tech bug.<br /> It is pity I found proteopedia after we published article on two protein-DNA structures.<br /> I will try in my Ph.D. thesis to visualise review of REase-DNA complexes with proteopedia.<br /> <br /> greatings from Vilne,<br /> Dima<br /> <br /> Now I see it was not bug but database case.<br /> <br /> ==molscript2Jmol==<br /> <br /> Hi,<br /> <br /> Is it possible simple coversion or implementation of molscript input and/or .mols files to Jmol script?</div>

Dima Golovenko https://proteopedia.org/index.php?title=User_talk:Eran_Hodis&diff=1014822 User talk:Eran Hodis 2009-11-09T12:35:55Z

<p>Dima Golovenko: /* Restriction endonucleases complexes with DNA - PspGI (3bm3) case */</p> <hr /> <div>==News from Greece==<br /> Hi Eran,<br /> actually I was on vacation after the summer school of Erice! <br /> The last days I'm back in the lab and try to find the rythm of the experiments ;)<br /> I shown to my boss the proteopedia and my page..he is excited! Actually I'm writing a paper and I may use the proteopedia for making the pictures. I would like to ask you how can I export the pictures to my pc.<br /> We'll be in contact..you'll see the progress of my page!<br /> <br /> best wishes<br /> Maria<br /> ---------<br /> <br /> <br /> Hi Eran,<br /> Now back at home with access to my Mac. Much enjoyed meeting and talking with you. Carole and I enjoyed our round trip of Sicily, and we more or less walked our feet off in Pompei last Monday. Off to practice our golf swings now. I also talked to one of the head honchos of the Cambridge small molecule crystallographic database, and he was receptive to the idea of making a filterered subset of drugs and other biologically-active small molecules available to Proteopedia (read: ligands). If you are ever in the neighbourhood of Basel, look us up, and we can offer you a free place to sleep.<br /> best regards<br /> Trevor<br /> ---------<br /> <br /> Hi Eran. How are you? I'm Maria Ambrazi..do you remember from Erice? Can you send me your e-mail...I would like to ask you something on proteopedia!<br /> <br /> == Bad green link ==<br /> Eran,<br /> I have a green link which does not work, it should make a Ramachandran plot. When I attempt to edit it the SAT freezes and no other scenes can be loaded. In fact as I remember when I first made the scene the SAT froze. After the SAT freezes some of the links above and below this bad link no longer work. Is there a way that a developer can delete scenes?<br /> <br /> Karl<br /> <br /> ---------<br /> After I left the message for you, I decided to take a different approach and not use the link, but I would be interested in knowing what is wrong with the link if you can discover that. I named the link plot_tripep_disallowed.<br /> <br /> Karl<br /> <br /> <br /> == PDBsum site ==<br /> Eran,<br /> After exploring this site I have come to the conclusion that the entry page to this site changes from time to time. Is that correct? If so, I should give directions on the Ramachandran page how to generate the Ramachandran plot on PDBsum.<br /> <br /> By the way that site is a wonderful resource. I am going to include it in the computer resource exercise that I have my Biochemistry I students do.<br /> <br /> Karl<br /> <br /> Eran,<br /> I just realized that I was not thinking clearly this morning. I had forgotten that the url that I am using is coded for 1eve and Procheck, and therefore the site will open with the desired protein and information displayed.<br /> <br /> Karl<br /> <br /> == Proteopedia for teaching ==<br /> Hi Eran<br /> <br /> I'm in the middle of my labs using Proteopedia, and on balance I think it's a great improvement for this class - I run 6 streams of 60 students each in a 2nd year biochemistry class. Using sPDBv meant that they spent a lot of time struggling with the program, but proteopedia is letting them just think about the protein structure instead. So, overall positive. However, two things that have come up:<br /> <br /> 1) Secondary structure definitions - How does Jmol generate them? Are they user definable? Jmol is clearly using a different algorithm to sPDBv, so students are seeing inconsistency when they use both routes. (For the record, I agree with sPDBv's pick!)<br /> <br /> 2) More seriously, the display of backbone hydrogen bonds is wrong - not sure if this is something I'm doing wrong or a fault in Jmol. Backbone hydrogen bonds are being drawn between C-alphas rather than between carbonyl oxygens and peptide nitrogens. Check out the link at the very bottom of the page http://www.proteopedia.org/wiki/index.php/User:J._Shaun_Lott/BIOSCI_203 marked "What is wrong with this picture?" to see what I mean.<br /> <br /> cheers!<br /> <br /> Shaun<br /> <br /> == What to do with my students contributions ==<br /> <br /> Hi Eran,<br /> <br /> I am trying user talk to communicate instead of my email, since my question may be relevant to other educators. I have several student contributions that I wish to keep and others that ought to be erased eventually. I want to keep the good ones, and one bad one for illustration of a range of student abilities. I am not sure if its best to transfer the material to my page; start another page with student contributions, or to link to the student's pages. I have the passwords the student sites, so I can access the scripts. What do you suggest is best?<br /> <br /> Tom<br /> <br /> == Surfaces ==<br /> <br /> Hi Eran,<br /> <br /> I tried but could not figure out if a surface of one protomer could be colored differently from a surface of another protomer using the surface representation.<br /> <br /> Tom<br /> <br /> == more on surfaces ==<br /> <br /> Hi<br /> <br /> Surfaces are slow to load--such is life--but my experience is the same as yours. Only one color is available for the surfaces.<br/><br /> my best<br/><br /> Tom<br/><br /> PS. So, what is the Israeli greetings/salutation during Hannukah?<br /> <br /> == Cheers Eran! ==<br /> <br /> Thanks for the info. About the template text - it even appears here when I click the + tab in your talk page. I think it should be easy enough to limit the feature by namespace, as many WP extensions seem to be ns specific. <br /> <br /> <br /> BTW, did you ever consider installing something like 'liquid threads' to make discussion more 'fully featured'? I played with it on a small wiki, and it worked OK, but when you install it you loose all old discussions. For a while I wanted to merge something like PHP BB with WP to create a forum 'channel' for each page, which should be simple enough to do... --[[User:Dan Bolser|Dan Bolser]] 10:58, 5 January 2009 (IST)<br /> <br /> == RE: ==<br /> <br /> <br /> Agreed about the template text. I'll email/message you when we have it updated. As to liquid threads, we've never considered anything like that, although its clear that the current MediaWiki system of messages is less than intuitive to say the least. We'd be hesitant to make large changes whose stability is not guaranteed, but if you think this is something we should look into, please link me to the appropriate places where I can read more about it. Eran Hodis 13:59, 5 January 2009 (IST) <br /> <br /> : With respect to 'is [this] something we should look into', I'm not really sure. It depends on how much you want Proteopedia to function as a 'community discussion forum' in addition to being a 'community education portal'. Actually, something like 'technical community discussion' was the emphasis of PDBWiki, which is why we think that it stands distinct from Proteopedia (with its emphasis on education). So basically I think its up to you to look at what is possible and assess the potential benefit, which may be marginal. Liquid threads is at http://www.mediawiki.org/wiki/Extension:LiquidThreads However, as I said, I'd be more interested in seeing a mini 'PHP BB' appearing within each talk tab http://www.phpbb.com/ I don't know why there are no efforts to implement this (that I can find). Oh... I spoke to soon ;-D http://www.mediawikiusers.com/wiki/index.php/Projects:MediaWiki/phpBB_Integration but that seems a bit thin on details TBH... Anyway, I only mentioned this because you seem to have a good capacity to work on such features, and I think that such a feature would be generally useful to the wider wiki world. All the best --[[User:Dan Bolser|Dan Bolser]] 15:24, 5 January 2009 (IST)<br /> <br /> :: After poking around I found this, http://www.mediawiki.org/wiki/Extension:AWC's_Forum which looks very promising. --[[User:Dan Bolser|Dan Bolser]] 16:00, 5 January 2009 (IST)<br /> <br /> ==RE: Models==<br /> <br /> Thanks Eran! We have been busier than expected at the CBM (but what else is new). Still, we hope to continue working on Proteopedia to upload more and more images of models we have developed - as well as some working SMART Team pages. Joel let me know that all the models made it to him intact so he should have them to show off when he gets back on your side of the world. It is a pretty neat collection of a very interesting topic - so enjoy!<br /> <br /> -Mark<br /> <br /> == Moving scenes from one page to another ==<br /> <br /> Hi Eran,<br /> <br /> I am able to copy wiki script from one page and copy it to another page using copy command: I can do ths copy <nowiki><scene>...<scene/></nowiki> (assuming I wrote the syntax correctly) from User:Tom Gluick/Human Glutamine Synthetase (section) to User:Tom Gluick/Human Glutamine Synthetase (section)/quaternary a subpage. However, I would like to change the scene in the subpage, but when SAT is access in subpage, the scene is not found associated with the subpage. is there something that can be done to remedy this issue. It would certainly save me time if this were possible.<br /> <br /> Tom<br /> <br /> ==Other Media in Proteopedia?==<br /> <br /> Hi Eran,<br /> <br /> I have a question about the potential for additional media on pages. I know we can easily load and display images on Proteopedia, but is there any way to upload other file varieties - for example, simple flash animations (.swf) or something similar to that? Or, if we can't actually upload them to the Proteopedia webspace, is there any way to have files uploaded on our own server and just displayed on the proteopedia page - perhaps by using some html similar to the <img src="www.filename.jpg"> code you can use for linking to images)?<br /> <br /> -Mark<br /> <br /> ===tilman ===<br /> Eran, you are right. That page <br /> Http://proteopedia.org/wiki/index.php/User:Tilman_Schirmer/Sandbox_10<br /> is obsolete. I've saved the content to the proper Sandbox_10.<br /> <br /> You can delete it. Thanks,<br /> Tilman<br /> ==References==<br /> <br /> Thanks for the tip Eran. I seem to stumble across cool built in features for Proteopedia like that every time I use it! Keep up the good work.<br /> <br /> -Mark<br /> <br /> == good enough? ==<br /> <br /> Would you say, [[User:Ralf Stephan/Sandbox 2|this]] is good enough to replace [[2a7g]]? What more does it need for a page 'Thermolysin'? --[[User:Ralf Stephan|Ralf Stephan]] 16:57, 7 February 2009 (IST)<br /> <br /> :It's certainly enough to replace [[2a7g]], and a great start! (please do replace it) The automatically added abstract here doesn't seem to have anything to do with the structure. Is this indeed the primary publication for the structure? Some questions/comments about your additions: Consider making "metalloprotease" as a interwiki link. We have a not-so-well developed page on [[Matrix_metalloproteinases]], but none on metalloproteases, so the reader may wonder what is a metalloprotease and what is its enzymatic function. It says "calcium atoms (yellow)" but I don't see any calcium atoms in yellow, they are green for me (as they usually are by default). It's not made entirely clear what the HEXHH motif is, could you clarify? I feel the reader would also wonder why is it important to mention in the first sentence that the protein contains zinc and several calcium atoms. Also, what is the substrate usually? The green links look just spectacular, and I'm glad to see you've quickly gotten the hang of the Scene Authoring Tools. <br /> <br /> :A page called 'Thermolysin' is a great idea, are there any other structures? We could transclude a section from your new [[2a7g]] page as well as elaborate more -- especially if there are other structures. --[[User:Eran Hodis|Eran Hodis]] 02:34, 8 February 2009 (IST)<br /> ::*There are lots of other thermolysin structures, mostly inhibitors docking and soaked with different solvent concentrations (why these?).<br /> :::Just thinking that a topic page on thermolysin could use the other structures as well to present a fuller picture.<br /> ::*So, a topic has a set of structures, ideally of all structures, with the structures pointing to 'their' nearest topic?<br /> :::That's the current mode of thinking. Of course better ideas will be adopted.<br /> ::*Regarding yellow/green, that's an example of me unconsciously giving away personal genetic data ;) Really, if I have that problem, other R/G blind people would have, too, so I'd suggest a different color for calcium.<br /> :::Hmm, yes we actually were wondering if that would be a problem when we made the scene links green -- is it a problem? Unfortunately it would be quite unfeasible to change from green scene links at this point. As far as changing calcium to a color other than green -- green might be part of a big coloring scheme that we might want to stick with. We can have a discussion on this if need be. <br /> ::*/Wrt the paper, that paper is given by PDBsum, too, one of those where the protein is just an example in a technical presentation. I should have used a different one.<br /> :::Ok, in this case then it is probably acceptable to leave out the publication abstract. If we use a more fitting abstract, but one from authors that did not solve that structure, it might send the wrong impression to readers that the wrong set of authors solved the structure. If you choose to do this, I would make it clear that the abstract is not the official one for this structure, and list the authors that did solve the structure with the appropriate reference.<br /> ::*Yes, MMPs are only a small subset of metalloproteases and should link to that WP article, too. <br /> :::Ok good.<br /> ::Thanks also for the other hints. Is there a list of all structure pages that have been enhanced manually? I know there's a manually maintained list as part of the topic page list but I think there should be something automatical such that enhancements are not lost. --[[User:Ralf Stephan|Ralf Stephan]] 10:16, 8 February 2009 (IST)<br /> :::Agreed, but the way to do this has slipped my mind at the moment. Let's see if Jaime Prilusky knows and will respond on the mailing list. --[[User:Eran Hodis|Eran Hodis]] 12:27, 8 February 2009 (IST)<br /> <br /> == java.io.File not found ==<br /> <br /> Do you understand why the applet can't find the PDB file in [[Helix-turn-helix motif]]? --[[User:Ralf Stephan|Ralf Stephan]] 17:57, 8 February 2009 (IST)<br /> :Never mind, I found it out myself: I forgot to provide a scene. --[[User:Ralf Stephan|Ralf Stephan]] 18:14, 8 February 2009 (IST)<br /> <br /> ==Image Issue==<br /> Hi Eran, <br /> I got your message and will take care of it. I think modified images were okay. <br /> Thanks!<br /> Leah<br /> <br /> ditto leah. thanks! becca<br /> <br /> ==Scrambled Eggs ==<br /> Any chance you are referring to egg cells and fertilization ? :)<br /> == Applet Behavior ==<br /> <br /> Eran, the applets in Z-DNA page seem to be behaving erratically. At times there <br /> is no display and at times they are not in the frame. There is also a problem<br /> with the sugar puckering option in DNA page. The applet freezes when this is selected.<br /> Could you please verify if you are facing the same problems?<br /> <br /> [[User:Adithya Sagar|Adithya Sagar]] 21:06, 22 October 2009 (IST)<br /> <br /> ==Image license==<br /> <br /> Originally from {Molecular cell biology. Lodish, Harvey 5 ed: - New York : W. H. Freeman and Co., 2003, 973 s. b ill. ISBN: 0-7167-4366-3. Libris: 8926100.}<br /> <br /> Original uploader was Roadnottaken at en.wikipedia 2007-03-22<br /> <br /> The image was found from Wikipedia and was a modified image that is a "GNU Free Documentation License"<br /> I changed the properties of my image file and it should give the proper acknowledgments.<br /> <br /> -Matt<br /> <br /> ==Restriction endonucleases complexes with DNA - PspGI (3bm3) case==<br /> <br /> Hi, Eran!<br /> <br /> It is nice to see such quick assistance with tech bug.<br /> It is pity I found proteopedia after we published article on two protein-DNA structures.<br /> I will try in my Ph.D. thesis to visualise review of REase-DNA complexes with proteopedia.<br /> <br /> greatings from Vilne,<br /> Dima<br /> <br /> Now I see it was not bug but database case.</div>

Dima Golovenko https://proteopedia.org/index.php?title=User_talk:Eran_Hodis&diff=1014821 User talk:Eran Hodis 2009-11-09T12:32:14Z

<p>Dima Golovenko: /* REases and DNA*/</p> <hr /> <div>==News from Greece==<br /> Hi Eran,<br /> actually I was on vacation after the summer school of Erice! <br /> The last days I'm back in the lab and try to find the rythm of the experiments ;)<br /> I shown to my boss the proteopedia and my page..he is excited! Actually I'm writing a paper and I may use the proteopedia for making the pictures. I would like to ask you how can I export the pictures to my pc.<br /> We'll be in contact..you'll see the progress of my page!<br /> <br /> best wishes<br /> Maria<br /> ---------<br /> <br /> <br /> Hi Eran,<br /> Now back at home with access to my Mac. Much enjoyed meeting and talking with you. Carole and I enjoyed our round trip of Sicily, and we more or less walked our feet off in Pompei last Monday. Off to practice our golf swings now. I also talked to one of the head honchos of the Cambridge small molecule crystallographic database, and he was receptive to the idea of making a filterered subset of drugs and other biologically-active small molecules available to Proteopedia (read: ligands). If you are ever in the neighbourhood of Basel, look us up, and we can offer you a free place to sleep.<br /> best regards<br /> Trevor<br /> ---------<br /> <br /> Hi Eran. How are you? I'm Maria Ambrazi..do you remember from Erice? Can you send me your e-mail...I would like to ask you something on proteopedia!<br /> <br /> == Bad green link ==<br /> Eran,<br /> I have a green link which does not work, it should make a Ramachandran plot. When I attempt to edit it the SAT freezes and no other scenes can be loaded. In fact as I remember when I first made the scene the SAT froze. After the SAT freezes some of the links above and below this bad link no longer work. Is there a way that a developer can delete scenes?<br /> <br /> Karl<br /> <br /> ---------<br /> After I left the message for you, I decided to take a different approach and not use the link, but I would be interested in knowing what is wrong with the link if you can discover that. I named the link plot_tripep_disallowed.<br /> <br /> Karl<br /> <br /> <br /> == PDBsum site ==<br /> Eran,<br /> After exploring this site I have come to the conclusion that the entry page to this site changes from time to time. Is that correct? If so, I should give directions on the Ramachandran page how to generate the Ramachandran plot on PDBsum.<br /> <br /> By the way that site is a wonderful resource. I am going to include it in the computer resource exercise that I have my Biochemistry I students do.<br /> <br /> Karl<br /> <br /> Eran,<br /> I just realized that I was not thinking clearly this morning. I had forgotten that the url that I am using is coded for 1eve and Procheck, and therefore the site will open with the desired protein and information displayed.<br /> <br /> Karl<br /> <br /> == Proteopedia for teaching ==<br /> Hi Eran<br /> <br /> I'm in the middle of my labs using Proteopedia, and on balance I think it's a great improvement for this class - I run 6 streams of 60 students each in a 2nd year biochemistry class. Using sPDBv meant that they spent a lot of time struggling with the program, but proteopedia is letting them just think about the protein structure instead. So, overall positive. However, two things that have come up:<br /> <br /> 1) Secondary structure definitions - How does Jmol generate them? Are they user definable? Jmol is clearly using a different algorithm to sPDBv, so students are seeing inconsistency when they use both routes. (For the record, I agree with sPDBv's pick!)<br /> <br /> 2) More seriously, the display of backbone hydrogen bonds is wrong - not sure if this is something I'm doing wrong or a fault in Jmol. Backbone hydrogen bonds are being drawn between C-alphas rather than between carbonyl oxygens and peptide nitrogens. Check out the link at the very bottom of the page http://www.proteopedia.org/wiki/index.php/User:J._Shaun_Lott/BIOSCI_203 marked "What is wrong with this picture?" to see what I mean.<br /> <br /> cheers!<br /> <br /> Shaun<br /> <br /> == What to do with my students contributions ==<br /> <br /> Hi Eran,<br /> <br /> I am trying user talk to communicate instead of my email, since my question may be relevant to other educators. I have several student contributions that I wish to keep and others that ought to be erased eventually. I want to keep the good ones, and one bad one for illustration of a range of student abilities. I am not sure if its best to transfer the material to my page; start another page with student contributions, or to link to the student's pages. I have the passwords the student sites, so I can access the scripts. What do you suggest is best?<br /> <br /> Tom<br /> <br /> == Surfaces ==<br /> <br /> Hi Eran,<br /> <br /> I tried but could not figure out if a surface of one protomer could be colored differently from a surface of another protomer using the surface representation.<br /> <br /> Tom<br /> <br /> == more on surfaces ==<br /> <br /> Hi<br /> <br /> Surfaces are slow to load--such is life--but my experience is the same as yours. Only one color is available for the surfaces.<br/><br /> my best<br/><br /> Tom<br/><br /> PS. So, what is the Israeli greetings/salutation during Hannukah?<br /> <br /> == Cheers Eran! ==<br /> <br /> Thanks for the info. About the template text - it even appears here when I click the + tab in your talk page. I think it should be easy enough to limit the feature by namespace, as many WP extensions seem to be ns specific. <br /> <br /> <br /> BTW, did you ever consider installing something like 'liquid threads' to make discussion more 'fully featured'? I played with it on a small wiki, and it worked OK, but when you install it you loose all old discussions. For a while I wanted to merge something like PHP BB with WP to create a forum 'channel' for each page, which should be simple enough to do... --[[User:Dan Bolser|Dan Bolser]] 10:58, 5 January 2009 (IST)<br /> <br /> == RE: ==<br /> <br /> <br /> Agreed about the template text. I'll email/message you when we have it updated. As to liquid threads, we've never considered anything like that, although its clear that the current MediaWiki system of messages is less than intuitive to say the least. We'd be hesitant to make large changes whose stability is not guaranteed, but if you think this is something we should look into, please link me to the appropriate places where I can read more about it. Eran Hodis 13:59, 5 January 2009 (IST) <br /> <br /> : With respect to 'is [this] something we should look into', I'm not really sure. It depends on how much you want Proteopedia to function as a 'community discussion forum' in addition to being a 'community education portal'. Actually, something like 'technical community discussion' was the emphasis of PDBWiki, which is why we think that it stands distinct from Proteopedia (with its emphasis on education). So basically I think its up to you to look at what is possible and assess the potential benefit, which may be marginal. Liquid threads is at http://www.mediawiki.org/wiki/Extension:LiquidThreads However, as I said, I'd be more interested in seeing a mini 'PHP BB' appearing within each talk tab http://www.phpbb.com/ I don't know why there are no efforts to implement this (that I can find). Oh... I spoke to soon ;-D http://www.mediawikiusers.com/wiki/index.php/Projects:MediaWiki/phpBB_Integration but that seems a bit thin on details TBH... Anyway, I only mentioned this because you seem to have a good capacity to work on such features, and I think that such a feature would be generally useful to the wider wiki world. All the best --[[User:Dan Bolser|Dan Bolser]] 15:24, 5 January 2009 (IST)<br /> <br /> :: After poking around I found this, http://www.mediawiki.org/wiki/Extension:AWC's_Forum which looks very promising. --[[User:Dan Bolser|Dan Bolser]] 16:00, 5 January 2009 (IST)<br /> <br /> ==RE: Models==<br /> <br /> Thanks Eran! We have been busier than expected at the CBM (but what else is new). Still, we hope to continue working on Proteopedia to upload more and more images of models we have developed - as well as some working SMART Team pages. Joel let me know that all the models made it to him intact so he should have them to show off when he gets back on your side of the world. It is a pretty neat collection of a very interesting topic - so enjoy!<br /> <br /> -Mark<br /> <br /> == Moving scenes from one page to another ==<br /> <br /> Hi Eran,<br /> <br /> I am able to copy wiki script from one page and copy it to another page using copy command: I can do ths copy <nowiki><scene>...<scene/></nowiki> (assuming I wrote the syntax correctly) from User:Tom Gluick/Human Glutamine Synthetase (section) to User:Tom Gluick/Human Glutamine Synthetase (section)/quaternary a subpage. However, I would like to change the scene in the subpage, but when SAT is access in subpage, the scene is not found associated with the subpage. is there something that can be done to remedy this issue. It would certainly save me time if this were possible.<br /> <br /> Tom<br /> <br /> ==Other Media in Proteopedia?==<br /> <br /> Hi Eran,<br /> <br /> I have a question about the potential for additional media on pages. I know we can easily load and display images on Proteopedia, but is there any way to upload other file varieties - for example, simple flash animations (.swf) or something similar to that? Or, if we can't actually upload them to the Proteopedia webspace, is there any way to have files uploaded on our own server and just displayed on the proteopedia page - perhaps by using some html similar to the <img src="www.filename.jpg"> code you can use for linking to images)?<br /> <br /> -Mark<br /> <br /> ===tilman ===<br /> Eran, you are right. That page <br /> Http://proteopedia.org/wiki/index.php/User:Tilman_Schirmer/Sandbox_10<br /> is obsolete. I've saved the content to the proper Sandbox_10.<br /> <br /> You can delete it. Thanks,<br /> Tilman<br /> ==References==<br /> <br /> Thanks for the tip Eran. I seem to stumble across cool built in features for Proteopedia like that every time I use it! Keep up the good work.<br /> <br /> -Mark<br /> <br /> == good enough? ==<br /> <br /> Would you say, [[User:Ralf Stephan/Sandbox 2|this]] is good enough to replace [[2a7g]]? What more does it need for a page 'Thermolysin'? --[[User:Ralf Stephan|Ralf Stephan]] 16:57, 7 February 2009 (IST)<br /> <br /> :It's certainly enough to replace [[2a7g]], and a great start! (please do replace it) The automatically added abstract here doesn't seem to have anything to do with the structure. Is this indeed the primary publication for the structure? Some questions/comments about your additions: Consider making "metalloprotease" as a interwiki link. We have a not-so-well developed page on [[Matrix_metalloproteinases]], but none on metalloproteases, so the reader may wonder what is a metalloprotease and what is its enzymatic function. It says "calcium atoms (yellow)" but I don't see any calcium atoms in yellow, they are green for me (as they usually are by default). It's not made entirely clear what the HEXHH motif is, could you clarify? I feel the reader would also wonder why is it important to mention in the first sentence that the protein contains zinc and several calcium atoms. Also, what is the substrate usually? The green links look just spectacular, and I'm glad to see you've quickly gotten the hang of the Scene Authoring Tools. <br /> <br /> :A page called 'Thermolysin' is a great idea, are there any other structures? We could transclude a section from your new [[2a7g]] page as well as elaborate more -- especially if there are other structures. --[[User:Eran Hodis|Eran Hodis]] 02:34, 8 February 2009 (IST)<br /> ::*There are lots of other thermolysin structures, mostly inhibitors docking and soaked with different solvent concentrations (why these?).<br /> :::Just thinking that a topic page on thermolysin could use the other structures as well to present a fuller picture.<br /> ::*So, a topic has a set of structures, ideally of all structures, with the structures pointing to 'their' nearest topic?<br /> :::That's the current mode of thinking. Of course better ideas will be adopted.<br /> ::*Regarding yellow/green, that's an example of me unconsciously giving away personal genetic data ;) Really, if I have that problem, other R/G blind people would have, too, so I'd suggest a different color for calcium.<br /> :::Hmm, yes we actually were wondering if that would be a problem when we made the scene links green -- is it a problem? Unfortunately it would be quite unfeasible to change from green scene links at this point. As far as changing calcium to a color other than green -- green might be part of a big coloring scheme that we might want to stick with. We can have a discussion on this if need be. <br /> ::*/Wrt the paper, that paper is given by PDBsum, too, one of those where the protein is just an example in a technical presentation. I should have used a different one.<br /> :::Ok, in this case then it is probably acceptable to leave out the publication abstract. If we use a more fitting abstract, but one from authors that did not solve that structure, it might send the wrong impression to readers that the wrong set of authors solved the structure. If you choose to do this, I would make it clear that the abstract is not the official one for this structure, and list the authors that did solve the structure with the appropriate reference.<br /> ::*Yes, MMPs are only a small subset of metalloproteases and should link to that WP article, too. <br /> :::Ok good.<br /> ::Thanks also for the other hints. Is there a list of all structure pages that have been enhanced manually? I know there's a manually maintained list as part of the topic page list but I think there should be something automatical such that enhancements are not lost. --[[User:Ralf Stephan|Ralf Stephan]] 10:16, 8 February 2009 (IST)<br /> :::Agreed, but the way to do this has slipped my mind at the moment. Let's see if Jaime Prilusky knows and will respond on the mailing list. --[[User:Eran Hodis|Eran Hodis]] 12:27, 8 February 2009 (IST)<br /> <br /> == java.io.File not found ==<br /> <br /> Do you understand why the applet can't find the PDB file in [[Helix-turn-helix motif]]? --[[User:Ralf Stephan|Ralf Stephan]] 17:57, 8 February 2009 (IST)<br /> :Never mind, I found it out myself: I forgot to provide a scene. --[[User:Ralf Stephan|Ralf Stephan]] 18:14, 8 February 2009 (IST)<br /> <br /> ==Image Issue==<br /> Hi Eran, <br /> I got your message and will take care of it. I think modified images were okay. <br /> Thanks!<br /> Leah<br /> <br /> ditto leah. thanks! becca<br /> <br /> ==Scrambled Eggs ==<br /> Any chance you are referring to egg cells and fertilization ? :)<br /> == Applet Behavior ==<br /> <br /> Eran, the applets in Z-DNA page seem to be behaving erratically. At times there <br /> is no display and at times they are not in the frame. There is also a problem<br /> with the sugar puckering option in DNA page. The applet freezes when this is selected.<br /> Could you please verify if you are facing the same problems?<br /> <br /> [[User:Adithya Sagar|Adithya Sagar]] 21:06, 22 October 2009 (IST)<br /> <br /> ==Image license==<br /> <br /> Originally from {Molecular cell biology. Lodish, Harvey 5 ed: - New York : W. H. Freeman and Co., 2003, 973 s. b ill. ISBN: 0-7167-4366-3. Libris: 8926100.}<br /> <br /> Original uploader was Roadnottaken at en.wikipedia 2007-03-22<br /> <br /> The image was found from Wikipedia and was a modified image that is a "GNU Free Documentation License"<br /> I changed the properties of my image file and it should give the proper acknowledgments.<br /> <br /> -Matt<br /> <br /> ==Restriction endonucleases complexes with DNA - PspGI (3bm3) case==<br /> <br /> Hi, Eran!<br /> <br /> It is nice to see such quick assistance with tech bug.<br /> It is pity I found proteopedia after we published article on two protein-DNA structures.<br /> I will try in my Ph.D. thesis to visualise review of REase-DNA complexes with proteopedia.<br /> <br /> greatings from Vilne,<br /> Dima</div>

Dima Golovenko