Proteopedia - User contributions [en]

https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Carrie+Morrison+Penland Proteopedia - User contributions [en] 2026-10-08T10:37:19Z User contributions MediaWiki 1.43.8 https://proteopedia.org/index.php?title=CBI_Molecules&diff=1878778 CBI Molecules 2013-12-20T23:22:42Z

<p>Carrie Morrison Penland: </p> <hr /> <div>These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].<br /> Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.<br /> <br /> UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.<br /> <br /> Fall 2013: CBI Molecules are due 12/4/13 and should be added at the TOP of the list from your lab. Label it as "in progress" until you are finished, and then as "New 2013" or "Revised 2013". For those editing an existing CBI Molecule, start from that entry so that it retains the full author list of all authors that contributed (or include credits to the original page and authors if it does not).<br /> <br /> <br /> ==Molecules==<br /> '''** Designates CBI Molecules Featured on [http://http://www.umass.edu/cbi/ CBI website]'''<br /> <br /> Bhatia Lab<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer<br /> <br /> <br /> [http://chamberslab.com/wp/ Chambers Lab]<br /> <br /> : '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano<br /> <br /> <br /> <br /> [http://www.chem.umass.edu/~chenlab/index.HTML Chen Lab]<br /> <br /> : Updated Fall 2013!! '''[[Molecular Playground/OmpG]]''', Christina Chisholm<br /> : New Fall 2013!! '''[[Molecular Playground/ClyA]]''', Bib Yang<br /> <br /> [http://openwetware.org/wiki/Chien Chien Lab]<br /> <br /> New Fall 2013! : **'''[[Molecular Playground/Homo-dimeric RcdA]]''', Kamal K. Joshi <br /> <br /> : **'''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau <br /> :: Best CBI Molecule 2011<br /> <br /> : '''[[Molecular Playground/DNA replication initiator DnaA]]''', Jing Liu<br /> <br /> <br /> Forbes Lab<br /> <br /> : '''[[Molecular Playground/CheR]]''', Miaomin Zhang<br /> <br /> : '''[[Molecular Playground/RBP]]''', Jan Panteli<br /> <br /> : '''[[Molecular Playground/TRAIL]]''', Charley Swofford<br /> <br /> <br /> [http://www.biochem.umass.edu/garman/index.html Garman Lab]<br /> <br /> : '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon<br /> <br /> : '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli<br /> <br /> <br /> [http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]<br /> <br /> : '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy<br /> :: Best Overall CBI Molecule 2010<br /> <br /> : '''[[Molecular Playground/CRABP I (Cellular Retinoic Acid Binding Protein)]]''', Gustavo Elberto Epalza Sanchez<br /> (compare this to the previous version above to see what's new)<br /> <br /> : **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani <br /> :: Best CBI Molecule 2012<br /> <br /> <br /> [http://people.chem.umass.edu/jhardy/ Hardy Lab]<br /> <br /> : New Fall 2013!! '''[[Molecular Playground/Executioner Caspase-7]]''', Derek MacPherson, Maureen E. Hill<br /> <br /> : '''[[Molecular Playground/[[Caspase-3 Regulatory Mechanisms]]''', Scott Eron, Bay Serrano, Yunlong Zhao<br /> <br /> : ''' [[Molecular Playground/Caspase-6 and neurodegeneration]]''', Kevin Buadlart Dagbay<br /> <br /> : '''[[Molecular Playground/Caspase-7 Dynamics]]'''<br /> <br /> : '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber<br /> <br /> : '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez<br /> <br /> : '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls<br /> <br /> : '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz<br /> <br /> <br /> Hebert Lab<br /> <br /> : New Fall 2013!! '''[[Molecular_Playground/Hsp70-Hsp90]]''', Jill Graham<br /> : New Fall 2012!! '''[[Molecular_Playground/ERDj5]]''', Lydia Lamriben<br /> : '''[[Molecular Playground/Saposin C]]''', Abla Tannous<br /> : '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd<br /> <br /> <br /> [http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]<br /> <br /> : Updated Fall 2012!! '''[[Molecular_Playground/Pcr H]]''', Fabian Romano, Carolina Morell-Pérez<br /> <br /> <br /> [http://people.chem.umass.edu/mholden/ Holden Lab]<br /> <br /> : New Fall 2012!! '''[[Molecular Playground/Protective Antigen]]''', Jing Huang<br /> <br /> <br /> <br /> [http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]<br /> <br /> New 2013! '''[http://proteopedia.org/wiki/index.php/Chengfeng_Ren Molecular Playground/Inteferon]''', Chengfeng Ren<br /> <br /> : Updated Fall 2012!! ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski<br /> <br /> : '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita<br /> <br /> <br /> <br /> <br /> Knapp lab<br /> <br /> : Updated Fall 2013!! '''[[Molecular Playground/FIH]]''', Vanessa Chaplin, Cornelius Taabazuing, Breanne Holmes, John Hangasky<br /> <br /> : Updated Fall 2012!! '''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas<br /> :: Best CBI Molecule Proteopedia Page 2010<br /> <br /> <br /> <br /> <br /> [http://people.chem.umass.edu/mmaroney/ Maroney Lab]<br /> <br /> : '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr<br /> : Updated Fall 2013!! '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu, Carolyn Carr<br /> : '''[[Molecular Playground/HypA]]''', Heidi Hu<br /> <br /> <br /> [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> : **'''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia <br /> :: Best CBI Molecule 2011<br /> : '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia<br /> <br /> : '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan <br /> <br /> <br /> [http://www.peytonlab.org/ Peyton Lab]<br /> : New Fall 2013! '''[[Molecular Playground/MMP14]]''', Lauren Jansen<br /> <br /> : '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen<br /> <br /> : '''[[Molecular Playground/FAK]]''', Dannielle Ryman<br /> <br /> [http://roberts.openwetware.org/ Roberts Lab]<br /> <br /> : '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson<br /> <br /> : '''[[Molecular Playground/Insulin]]''', Whitney Stoppel<br /> <br /> <br /> [http://www.umass.edu/rotellogroup/ Rotello Lab]<br /> <br /> : '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino<br /> <br /> : '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang<br /> <br /> : '''[[Molecular playground/Chymotrypsin]]''', Brad<br /> <br /> : '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell<br /> <br /> [http://http://www.umass.edu/schiffman/ Schiffman Lab]<br /> :New Fall 2013! '''[[Molecular Playground/Streptavidin]]''', Katrina Rieger<br /> <br /> [https://elements.chem.umass.edu/schnarrlab/ Schnarr Lab] <br /> <br /> : New Fall 2012!! '''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey <br /> <br /> : '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso, Lawrence Sheringham Borketey<br /> <br /> : '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad<br /> <br /> <br /> [http://www.biochem.umass.edu/faculty/danny-j-schnell Schnell Lab]<br /> : New Fall 2012!! '''[[Molecular Playground/Tic40]]''', Mine Canakci<br /> <br /> <br /> <br /> <br /> Tew Lab<br /> <br /> : Updated Fall 2013!! '''[[Molecular Playground/HIV Tat]]''', Brittany deRonde<br /> <br /> <br /> Thayumanavan Lab<br /> : New Fall 2013!! '''[[Interleukin-1 beta]]''', Huan He<br /> <br /> : '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez<br /> <br /> : '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura<br /> <br /> : '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi<br /> <br /> : '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy<br /> <br /> : '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado <br /> <br /> : '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang<br /> <br /> : ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo<br /> <br /> : '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko<br /> <br /> Thayumanavan & Vachet Labs<br /> <br /> : '''[[Molecular Playground/Trypsin]]''', Gladys Murage<br /> <br /> <br /> [http://people.chem.umass.edu/thompson/index.html Thompson] & [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs<br /> <br /> : New Fall 2013!! '''[[Molecular Playground/Bacterial Chemotaxis Complex]]''', Elizabeth R. Haglin<br /> <br /> : New Fall 2012!! '''[[Molecular Playground/CheA]]''', Elizabeth R. Haglin<br /> <br /> : '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones<br /> <br /> : '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang<br /> <br /> : '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li<br /> <br /> <br /> [http://www.chem.umass.edu/~vachet/index.html Vachet Lab]<br /> <br /> : New Fall 2013!! '''[[Molecular Playground/Human Serum Albumin]]''', Mahalia Serrano<br /> <br /> : '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto<br /> :: Best CBI Molecule Jmol scenes 2010<br /> <br /> : '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou <br /> <br /> :'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne<br /> <br /> : '''[[Molecular Playground/Ubiquitin salt bridge discussion]]''', Zhe Zhang<br /> <br /> <br /> Other Molecules of interest<br /> <br /> : '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> <br /> Other Laboratories<br /> <br /> : '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]<br /> <br /> : '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab<br /> <br /> : '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab<br /> <br /> ==Instructions==<br /> <br /> '''The goal is for students to work collaboratively to create one excellent CBI Molecule for each CBI research group, to be featured on the CBI website.'''<br /> <br /> Fall 2013: Complete steps 1-2 by 10/18, and bring your computer to the CBI Molecule Workshop on Wed 10/23 in ISB 321. <br /> <br /> A successful CBI Molecule will be an interesting, nontechnical description of a molecule related to your group's research. It should not be super long, but instead have multiple green scenes. Green scenes should clearly show an interesting feature and should be attractive. Use the green scenes to help you make interesting points about the molecule (do not try to describe every feature of the molecule). It's great if you can end with a brief statement about how it relates to your group's research goals.<br /> <br /> 1. If you don't already have one, request a Proteopedia account and log in. <br /> <br /> 2. Read through the rest of the instructions and look at any existing CBI Molecules from your research group. Talk with other Chalk Talk students in your research group and think about how you can make a new or improved CBI Molecule related to your group's research. Develop ideas for the scenes you wish to show. You will work learn how to make scenes during the workshop. <br /> <br /> 3. Get started working in Proteopedia by using the links at [[Help:Contents]]. Make yourself a sandbox page: Enter "User:Your Name/Sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. Practice entering text, inserting a structure window with scrolling text (green 4-square button on the right), and creating a green scene. You can look at other Proteopedia pages in edit mode to see how different effects (like colored text) are achieved (but this won't show you how the scene effects are made). <br /> <br /> 4. For those editing an existing CBI Molecule, start from that entry so that it retains the full author list of all authors that contributed. You are encouraged to collaborate on the CBI Molecules, but everyone will need to do some editing of the molecule so that they each appear as authors on the final list. If you are the sole student from your group enrolled in Chalk Talk and have not previously made a CBI Molecule, try to convince another group member who has previously made a CBI Molecule (see list above) to join us for the workshop so that you can work together.<br /> <br /> 5. Your final pages should be called "Molecular Playground/your molecule" and should have links on this CBI Molecule page -- put the new ones first on the list from your research group. Label them "in progress" until you are finished, and then "new 2013" or "revised 2013".<br /> <br /> ==Links to HELP pages==<br /> Overview at [[Help:Contents ]]<br /> <br /> See also [[Help:Getting_Started_in_Proteopedia]] <br /> <br /> Videos showing how to use Proteopedia:<br /> [[Proteopedia:Video_Guide]]<br /> (Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)<br /> <br /> [[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]<br /> gives succinct step by step instructions on how to create a molecular scene.<br /> <br /> A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.<br /> [http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]<br /> <br /> [[Proteopedia:Guidelines for Ethical Writing]].<br /> Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.<br /> <br /> For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.</div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=CBI_Molecules&diff=1872372 CBI Molecules 2013-12-04T17:41:24Z

<p>Carrie Morrison Penland: </p> <hr /> <div>These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].<br /> Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.<br /> <br /> UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.<br /> <br /> Fall 2013: CBI Molecules are due 12/4/13 and should be added at the TOP of the list from your lab. Label it as "in progress" until you are finished, and then as "New 2013" or "Revised 2013". For those editing an existing CBI Molecule, start from that entry so that it retains the full author list of all authors that contributed (or include credits to the original page and authors if it does not).<br /> <br /> <br /> ==Molecules==<br /> '''** Designates CBI Molecules Featured on [http://http://www.umass.edu/cbi/ CBI website]'''<br /> <br /> Bhatia Lab<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer<br /> <br /> <br /> [http://chamberslab.com/wp/ Chambers Lab]<br /> <br /> : '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano<br /> <br /> <br /> <br /> [http://www.chem.umass.edu/~chenlab/index.HTML Chen Lab]<br /> <br /> : New Fall 2012!! '''[[Molecular Playground/OmpG]]''', Christina Chisholm<br /> <br /> <br /> [http://openwetware.org/wiki/Chien Chien Lab]<br /> <br /> New Fall 2013! : **'''[[Molecular Playground/Homo-dimeric RcdA]]''', Kamal K. Joshi <br /> <br /> : **'''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau <br /> :: Best CBI Molecule 2011<br /> <br /> : '''[[Molecular Playground/DNA replication initiator DnaA]]''', Jing Liu<br /> <br /> <br /> Forbes Lab<br /> <br /> : '''[[Molecular Playground/CheR]]''', Miaomin Zhang<br /> <br /> : '''[[Molecular Playground/RBP]]''', Jan Panteli<br /> <br /> : '''[[Molecular Playground/TRAIL]]''', Charley Swofford<br /> <br /> <br /> [http://www.biochem.umass.edu/garman/index.html Garman Lab]<br /> <br /> : '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon<br /> <br /> : '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli<br /> <br /> <br /> [http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]<br /> <br /> : '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy<br /> :: Best Overall CBI Molecule 2010<br /> <br /> : '''[[Molecular Playground/CRABP I (Cellular Retinoic Acid Binding Protein)]]''', Gustavo Elberto Epalza Sanchez<br /> (compare this to the previous version above to see what's new)<br /> <br /> : **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani <br /> :: Best CBI Molecule 2012<br /> <br /> <br /> [http://people.chem.umass.edu/jhardy/ Hardy Lab]<br /> <br /> : New Fall 2013!! '''[[Molecular Playground/Executioner Caspase-7]]''', Derek MacPherson, Maureen E. Hill<br /> <br /> : '''[[Molecular Playground/[[Caspase-3 Regulatory Mechanisms]]''', Scott Eron, Bay Serrano, Yunlong Zhao<br /> <br /> : ''' [[Molecular Playground/Caspase-6 and neurodegeneration]]''', Kevin Buadlart Dagbay<br /> <br /> : '''[[Molecular Playground/Caspase-7 Dynamics]]'''<br /> <br /> : '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber<br /> <br /> : '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez<br /> <br /> : '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls<br /> <br /> : '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz<br /> <br /> <br /> Hebert Lab<br /> <br /> : New Fall 2013!! '''[[Molecular_Playground/Hsp70-Hsp90]]''', Jill Graham<br /> : New Fall 2012!! '''[[Molecular_Playground/ERDj5]]''', Lydia Lamriben<br /> : '''[[Molecular Playground/Saposin C]]''', Abla Tannous<br /> : '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd<br /> <br /> <br /> [http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]<br /> <br /> : Updated Fall 2012!! '''[[Molecular_Playground/Pcr H]]''', Fabian Romano, Carolina Morell-Pérez<br /> <br /> <br /> [http://people.chem.umass.edu/mholden/ Holden Lab]<br /> <br /> : New Fall 2012!! '''[[Molecular Playground/Protective Antigen]]''', Jing Huang<br /> <br /> <br /> <br /> [http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]<br /> <br /> : Updated Fall 2012!! ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski<br /> <br /> : '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita<br /> <br /> <br /> <br /> Knapp lab<br /> <br /> : Updated Fall 2013!! '''[[Molecular Playground/FIH]]''', Vanessa Chaplin, Cornelius Taabazuing, Breanne Holmes, John Hangasky<br /> <br /> : Updated Fall 2012!! '''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas<br /> :: Best CBI Molecule Proteopedia Page 2010<br /> <br /> <br /> <br /> <br /> [http://people.chem.umass.edu/mmaroney/ Maroney Lab]<br /> <br /> : '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr<br /> : Updated Fall 2013!! '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu, Carolyn Carr<br /> : '''[[Molecular Playground/HypA]]''', Heidi Hu<br /> <br /> <br /> [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> : **'''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia <br /> :: Best CBI Molecule 2011<br /> : '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia<br /> <br /> : '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan <br /> <br /> <br /> [http://www.peytonlab.org/ Peyton Lab]<br /> : '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen<br /> : '''[[Molecular Playground/FAK]]''', Dannielle Ryman<br /> : New Fall 2013! '''[[Molecular Playground/MMP14]]''', Lauren Jansen<br /> <br /> [http://roberts.openwetware.org/ Roberts Lab]<br /> <br /> : '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson<br /> <br /> : '''[[Molecular Playground/Insulin]]''', Whitney Stoppel<br /> <br /> <br /> [http://www.umass.edu/rotellogroup/ Rotello Lab]<br /> <br /> : '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino<br /> <br /> : '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang<br /> <br /> : '''[[Molecular playground/Chymotrypsin]]''', Brad<br /> <br /> : '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell<br /> <br /> [http://http://www.umass.edu/schiffman/ Schiffman Lab]<br /> :New Fall 2013! '''[[Molecular Playground/Streptavidin]]''', Katrina Rieger<br /> <br /> [https://elements.chem.umass.edu/schnarrlab/ Schnarr Lab] <br /> <br /> : New Fall 2012!! '''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey <br /> <br /> : '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso, Lawrence Sheringham Borketey<br /> <br /> : '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad<br /> <br /> <br /> [http://www.biochem.umass.edu/faculty/danny-j-schnell Schnell Lab]<br /> : New Fall 2012!! '''[[Molecular Playground/Tic40]]''', Mine Canakci<br /> <br /> <br /> <br /> <br /> Tew Lab<br /> <br /> : '''[[Molecular Playground/HIV Tat]]''', Brittany deRonde<br /> <br /> <br /> Thayumanavan Lab<br /> <br /> : '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez<br /> <br /> : '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura<br /> <br /> : '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi<br /> <br /> : '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy<br /> <br /> : '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado <br /> <br /> : '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang<br /> <br /> : ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo<br /> <br /> : '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko<br /> <br /> <br /> Thayumanavan & Vachet Labs<br /> <br /> : '''[[Molecular Playground/Trypsin]]''', Gladys Murage<br /> <br /> <br /> [http://people.chem.umass.edu/thompson/index.html Thompson] & [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs<br /> <br /> : New Fall 2012!! '''[[Molecular Playground/CheA]]''', Elizabeth R. Haglin<br /> <br /> : '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones<br /> <br /> : '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang<br /> <br /> : '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li<br /> <br /> <br /> [http://www.chem.umass.edu/~vachet/index.html Vachet Lab]<br /> <br /> : '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto<br /> :: Best CBI Molecule Jmol scenes 2010<br /> <br /> : '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou <br /> <br /> :'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne<br /> <br /> : New Fall 2012!! '''[[Molecular Playground/Ubiquitin salt bridge discussion]]''', Zhe Zhang<br /> <br /> <br /> Other Molecules of interest<br /> <br /> : '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> <br /> Other Laboratories<br /> <br /> : '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]<br /> <br /> : '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab<br /> <br /> : '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab<br /> <br /> ==Instructions==<br /> <br /> '''The goal is for students to work collaboratively to create one excellent CBI Molecule for each CBI research group, to be featured on the CBI website.'''<br /> <br /> Fall 2013: Complete steps 1-2 by 10/18, and bring your computer to the CBI Molecule Workshop on Wed 10/23 in ISB 321. <br /> <br /> A successful CBI Molecule will be an interesting, nontechnical description of a molecule related to your group's research. It should not be super long, but instead have multiple green scenes. Green scenes should clearly show an interesting feature and should be attractive. Use the green scenes to help you make interesting points about the molecule (do not try to describe every feature of the molecule). It's great if you can end with a brief statement about how it relates to your group's research goals.<br /> <br /> 1. If you don't already have one, request a Proteopedia account and log in. <br /> <br /> 2. Read through the rest of the instructions and look at any existing CBI Molecules from your research group. Talk with other Chalk Talk students in your research group and think about how you can make a new or improved CBI Molecule related to your group's research. Develop ideas for the scenes you wish to show. You will work learn how to make scenes during the workshop. <br /> <br /> 3. Get started working in Proteopedia by using the links at [[Help:Contents]]. Make yourself a sandbox page: Enter "User:Your Name/Sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. Practice entering text, inserting a structure window with scrolling text (green 4-square button on the right), and creating a green scene. You can look at other Proteopedia pages in edit mode to see how different effects (like colored text) are achieved (but this won't show you how the scene effects are made). <br /> <br /> 4. For those editing an existing CBI Molecule, start from that entry so that it retains the full author list of all authors that contributed. You are encouraged to collaborate on the CBI Molecules, but everyone will need to do some editing of the molecule so that they each appear as authors on the final list. If you are the sole student from your group enrolled in Chalk Talk and have not previously made a CBI Molecule, try to convince another group member who has previously made a CBI Molecule (see list above) to join us for the workshop so that you can work together.<br /> <br /> 5. Your final pages should be called "Molecular Playground/your molecule" and should have links on this CBI Molecule page -- put the new ones first on the list from your research group. Label them "in progress" until you are finished, and then "new 2013" or "revised 2013".<br /> <br /> ==Links to HELP pages==<br /> Overview at [[Help:Contents ]]<br /> <br /> See also [[Help:Getting_Started_in_Proteopedia]] <br /> <br /> Videos showing how to use Proteopedia:<br /> [[Proteopedia:Video_Guide]]<br /> (Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)<br /> <br /> [[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]<br /> gives succinct step by step instructions on how to create a molecular scene.<br /> <br /> A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.<br /> [http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]<br /> <br /> [[Proteopedia:Guidelines for Ethical Writing]].<br /> Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.<br /> <br /> For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.</div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=User_talk:Jill_Graham&diff=1872371 User talk:Jill Graham 2013-12-04T17:36:20Z

<p>Carrie Morrison Penland: User talk:Jill Graham moved to Talk:Molecular Playground/Hsp70-Hsp90</p> <hr /> <div>#REDIRECT [[Talk:Molecular Playground/Hsp70-Hsp90]]</div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=Talk:Molecular_Playground/Hsp70-Hsp90&diff=1872370 Talk:Molecular Playground/Hsp70-Hsp90 2013-12-04T17:36:20Z

<p>Carrie Morrison Penland: User talk:Jill Graham moved to Talk:Molecular Playground/Hsp70-Hsp90</p> <hr /> <div>'''Welcome to ''Proteopedia''!''' We hope you will contribute much and well. You will probably want to watch the narrated [[Proteopedia:Video_Guide|video guide]] and use the [[Help:Contents|help pages]] for later reference. Again, welcome and have fun! . [[User:Eric Martz|Eric Martz]] 14:08, 24 October 2013 (IST)</div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=User:Jill_Graham&diff=1872369 User:Jill Graham 2013-12-04T17:36:20Z

<p>Carrie Morrison Penland: User:Jill Graham moved to Molecular Playground/Hsp70-Hsp90</p> <hr /> <div>#REDIRECT [[Molecular Playground/Hsp70-Hsp90]]</div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=Molecular_Playground/Hsp70-Hsp90&diff=1872368 Molecular Playground/Hsp70-Hsp90 2013-12-04T17:36:20Z

<p>Carrie Morrison Penland: User:Jill Graham moved to Molecular Playground/Hsp70-Hsp90</p> <hr /> <div><Structure load='Insert PDB code or filename here' size='500' frame='true' align='right' caption='TPR1' scene='56/566505/Tpr1/2' /><br /> <br /> <br /> ==Hsp70-Hsp90 Organizing Protein (Hop)==<br /> Hop is an adaptor protein that mediates the association of the molecular chaperones Hsp70 and Hsp90 as some proteins require their coordinated activities for folding and conformational regulation. Hsp90 receives its substrates from Hsp70 in a reaction that is critically dependent on Hop, but how Hop mediates this dual chaperone binding was unclear until structural studies of Hop were conducted. Hop is not a chaperone itself, and it is composed almost entirely of Tetra-trico-peptide repeat (TPR) domains. TPR domains are defined as multiple repeats of 34 amino acids that share a degenerate consensus sequence consisting of a pattern of small and large hydrophobic amino acids, with no position being completely invariant. TPR domains are found in many proteins and often serve as interaction modules in multiprotein complexes. Hop is a 543 amino acid protein with 9 predicted TPR motifs, which are organized into 3 TPR domains: TPR1, TPR2A, and TPR2B. <br /> <br /> ==TPR Domain 1 Structure==<br /> <scene name='56/566505/Tpr1/2'>TPR1</scene> consists of 3 <scene name='56/566505/Tpr_motifs/2'>TPR motifs</scene> and is responsible for the interaction with the C terminus of Hsp70 (motifs are colored red, blue, and purple respectively, and the C-terminal capping helix is shown in green). Mutation studies showed that the binding of TPR1 to Hsp70 is dependent upon the interaction between the TPR1 domain and a 12-mer C-terminal peptide of Hsp70 (GSGSGPTIEEVD). Shown to the right is the crystallized TPR1 with its respective Hsp70 heptapeptide partner. TPR1 forms a cradle-like structure that accommodates the Hsp70 peptide in an extended conformation, and the peptide makes contact with only the sidechains of the helices in TPR1 that face the inner surface of the cradle. Additionally, a highly conserved <scene name='56/566505/Cbxy_clamp/3'>two-carboxylate clamp</scene> anchors the EEVD peptide motif of Hsp70 to TPR1 (residues highlighted in orange). <br /> <br /> <br /> ==References==<br /> <br /> 1. D'Andrea, L. Regan, L. TiBS Review; 28:12. 2003 <br /> <br /> 2. Scheufler, C. et. al. Cell; 101:199-210. 2000<br /> <br /> 3. Zeytuni, N. et. al. Cell Structure; 20. 2012</div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=CBI_Molecules&diff=1635173 CBI Molecules 2012-12-17T18:46:06Z

<p>Carrie Morrison Penland: </p> <hr /> <div>These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].<br /> Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.<br /> <br /> UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.<br /> <br /> Fall 2012: CBI Molecules are due 12/12/12 and should be added at the TOP of the list from your lab. Label it as "in progress" until you are finished. For those editing an existing CBI Molecule, start from that entry so that it retains the full author list of all authors that contributed (or include credits to the original page and authors if it does not -- I may be able to request additions to the author list).<br /> <br /> <br /> ==Molecules==<br /> '''** Designates CBI Molecules Featured on [http://http://www.umass.edu/cbi/ CBI website]'''<br /> <br /> Bhatia Lab<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer<br /> <br /> <br /> [http://chamberslab.com/wp/ Chambers Lab]<br /> <br /> : '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano<br /> <br /> <br /> <br /> [http://www.chem.umass.edu/~chenlab/index.HTML Chen Lab]<br /> <br /> : New Fall 2012!! '''[[Molecular Playground/OmpG]]''', Christina Chisholm<br /> <br /> <br /> [http://openwetware.org/wiki/Chien Chien Lab]<br /> <br /> : **'''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau <br /> :: Best CBI Molecule 2011<br /> <br /> : '''[[Molecular Playground/DNA replication initiator DnaA]]''', Jing Liu<br /> <br /> <br /> Forbes Lab<br /> <br /> : '''[[Molecular Playground/CheR]]''', Miaomin Zhang<br /> <br /> : '''[[Molecular Playground/RBP]]''', Jan Panteli<br /> <br /> : '''[[Molecular Playground/TRAIL]]''', Charley Swofford<br /> <br /> <br /> [http://www.biochem.umass.edu/garman/index.html Garman Lab]<br /> <br /> : '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon<br /> <br /> : '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli<br /> <br /> <br /> [http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]<br /> <br /> : '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy<br /> :: Best Overall CBI Molecule 2010<br /> <br /> : '''[[Molecular Playground/CRABP I (Cellular Retinoic Acid Binding Protein)]]''', Gustavo Elberto Epalza Sanchez<br /> (compare this to the previous version above to see what's new)<br /> <br /> : **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani <br /> :: Best CBI Molecule 2012<br /> <br /> <br /> [http://people.chem.umass.edu/jhardy/ Hardy Lab]<br /> <br /> : New Fall 2012!! ''' [[Molecular Playground/[[Caspase-3 Regulatory Mechanisms]]''', Scott Eron, Bay Serrano, Yunlong Zhao<br /> <br /> : ''' [[Molecular Playground/Caspase-6 and neurodegeneration]]''', Kevin Buadlart Dagbay<br /> <br /> : '''[[Molecular Playground/Caspase-7 Dynamics]]'''<br /> <br /> : '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber<br /> <br /> : '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez<br /> <br /> : '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls<br /> <br /> : '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz<br /> <br /> <br /> Hebert Lab<br /> <br /> : New Fall 2012!! '''[[Molecular_Playground/ERDj5]]''', Lydia Lamriben<br /> : '''[[Molecular Playground/Saposin C]]''', Abla Tannous<br /> : '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd<br /> <br /> <br /> [http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]<br /> <br /> : '''[[Molecular_Playground/Pcr H]]''', Fabian Romano<br /> <br /> <br /> [http://people.chem.umass.edu/mholden/ Holden Lab]<br /> <br /> : New Fall 2012!! '''[[Molecular Playground/Protective Antigen]]''', Jing Huang<br /> <br /> <br /> <br /> [http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]<br /> <br /> : Updated Fall 2012!! ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski<br /> <br /> : '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita<br /> <br /> <br /> <br /> Knapp lab<br /> <br /> : Updated Fall 2012!! '''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas<br /> :: Best CBI Molecule Proteopedia Page 2010<br /> <br /> : '''[[Molecular Playground/FIH]]''', Cornelius Taabazuing, Breanne Holmes, John Hangasky<br /> <br /> <br /> [http://people.chem.umass.edu/mmaroney/ Maroney Lab]<br /> <br /> : New Fall 2012!! '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr<br /> : '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu<br /> : New Fall 2012!! '''[[Molecular Playground/HypA]]''', Heidi Hu<br /> <br /> <br /> [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> : **'''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia <br /> :: Best CBI Molecule 2011<br /> : '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia<br /> <br /> : '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan <br /> <br /> <br /> Peyton Lab<br /> : '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen<br /> : '''[[Molecular Playground/FAK]]''', Dannielle Ryman<br /> <br /> <br /> [http://roberts.openwetware.org/ Roberts Lab]<br /> <br /> : '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson<br /> <br /> : '''[[Molecular Playground/Insulin]]''', Whitney Stoppel<br /> <br /> <br /> [http://www.umass.edu/rotellogroup/ Rotello Lab]<br /> <br /> : '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino<br /> <br /> : '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang<br /> <br /> : '''[[Molecular playground/Chymotrypsin]]''', Brad<br /> <br /> : '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell<br /> <br /> <br /> <br /> [https://elements.chem.umass.edu/schnarrlab/ Schnarr Lab] <br /> <br /> : New Fall 2012!! '''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey <br /> <br /> : '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso<br /> <br /> : '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad<br /> <br /> <br /> Tew Lab<br /> <br /> : '''[[Molecular Playground/HIV Tat]]''', Brittany deRonde<br /> <br /> <br /> Thayumanavan Lab<br /> <br /> : '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez<br /> <br /> : '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura<br /> <br /> : '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi<br /> <br /> : '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy<br /> <br /> : '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado <br /> <br /> : '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang<br /> <br /> : ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo<br /> <br /> : '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko<br /> <br /> <br /> Thayumanavan & Vachet Labs<br /> <br /> : '''[[Molecular Playground/Trypsin]]''', Gladys Murage<br /> <br /> <br /> [http://people.chem.umass.edu/thompson/index.html Thompson] & [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs<br /> <br /> : New Fall 2012!! '''[[Molecular Playground/CheA]]''', Elizabeth R. Haglin<br /> <br /> : '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones<br /> <br /> : '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang<br /> <br /> : '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li<br /> <br /> <br /> [http://www.chem.umass.edu/~vachet/index.html Vachet Lab]<br /> <br /> : '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto<br /> :: Best CBI Molecule Jmol scenes 2010<br /> <br /> : '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou <br /> <br /> :'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne<br /> <br /> : New Fall 2012!! '''[[Ubiquitin salt bridge discussion]]''', Zhe Zhang<br /> <br /> <br /> Other Molecules of interest<br /> <br /> : '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> <br /> Other Laboratories<br /> <br /> : '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]<br /> <br /> : '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab<br /> <br /> : '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab<br /> <br /> ==Instructions==<br /> <br /> '''Congratulations to the prize-winning CBI molecules noted above! The new goal is for students to work collaboratively to create one excellent CBI Molecule for each CBI research group, to be featured on the CBI website.'''<br /> <br /> Fall 2012: Complete steps 1-3 by 10/10/12, in preparation for the CBI Molecule Workshop.<br /> <br /> 1. If you don't already have one, request a Proteopedia account and log in. <br /> <br /> 2. Get started working in Proteopedia by using the links at [[Help:Contents]]. Make yourself a sandbox page: Enter "User:Your Name/Sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. Practice entering text, inserting a structure window with scrolling text (green 4-square button on the right), and creating a green scene. You can look at other Proteopedia pages in edit mode to see how different effects (like colored text) are achieved (but this won't show you how the scene effects are made). <br /> <br /> 3. Get together with the other Chalk Talk students in your research group and decide which molecule you will improve or create. Develop ideas for the scenes you wish to show. You will work on these during the workshop with our help, and then finish them on your own.<br /> <br /> You are encouraged to collaborate on this year's CBI Molecules, but everyone will need to do some editing of the molecule so that they each appear as authors on the final list. If you are the sole student from your group enrolled in Chalk Talk and have not previously made a CBI Molecule, try to convince another group member who has previously made a CBI Molecule (see list above) to join us for the workshop so that you can work together.<br /> <br /> A successful CBI Molecule will be an interesting, nontechnical description of a molecule related to your group's research. It should not be super long, but instead have multiple green scenes. Green scenes should clearly show an interesting feature and should be attractive. Use the green scenes to help you make interesting points about the molecule (do not try to describe every feature of the molecule). It's great if you can end with a brief statement about how it relates to your group's research goals.<br /> <br /> 4. Your final pages should be called "Molecular Playground/your molecule" and should have links on this CBI Molecule page -- put the new ones first on the list from your research group. Label them "in progress" until you are finished.<br /> <br /> ==Links to HELP pages==<br /> Overview at [[Help:Contents ]]<br /> <br /> See also [[Help:Getting_Started_in_Proteopedia]] <br /> <br /> Videos showing how to use Proteopedia:<br /> [[Proteopedia:Video_Guide]]<br /> (Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)<br /> <br /> [[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]<br /> gives succinct step by step instructions on how to create a molecular scene.<br /> <br /> A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.<br /> [http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]<br /> <br /> [[Proteopedia:Guidelines for Ethical Writing]].<br /> Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.<br /> <br /> For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.</div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=CBI_Molecules&diff=1635148 CBI Molecules 2012-12-17T18:33:18Z

<p>Carrie Morrison Penland: </p> <hr /> <div>These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].<br /> Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.<br /> <br /> UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.<br /> <br /> Fall 2012: CBI Molecules are due 12/12/12 and should be added at the TOP of the list from your lab. Label it as "in progress" until you are finished. For those editing an existing CBI Molecule, start from that entry so that it retains the full author list of all authors that contributed (or include credits to the original page and authors if it does not -- I may be able to request additions to the author list).<br /> <br /> <br /> ==Molecules==<br /> '''** Designates CBI Molecules Featured on [http://http://www.umass.edu/cbi/ CBI website]'''<br /> <br /> Bhatia Lab<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer<br /> <br /> <br /> [http://chamberslab.com/wp/ Chambers Lab]<br /> <br /> : '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano<br /> <br /> <br /> <br /> [http://www.chem.umass.edu/~chenlab/index.HTML Chen Lab]<br /> <br /> : New Fall 2012!! '''[[Molecular Playground/OmpG]]''', Christina Chisholm<br /> <br /> <br /> [http://openwetware.org/wiki/Chien Chien Lab]<br /> <br /> : **'''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau <br /> :: Best CBI Molecule 2011<br /> <br /> : '''[[Molecular Playground/DNA replication initiator DnaA]]''', Jing Liu<br /> <br /> <br /> Forbes Lab<br /> <br /> : '''[[Molecular Playground/CheR]]''', Miaomin Zhang<br /> <br /> : '''[[Molecular Playground/RBP]]''', Jan Panteli<br /> <br /> : '''[[Molecular Playground/TRAIL]]''', Charley Swofford<br /> <br /> <br /> [http://www.biochem.umass.edu/garman/index.html Garman Lab]<br /> <br /> : '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon<br /> <br /> : '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli<br /> <br /> <br /> [http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]<br /> <br /> : '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy<br /> :: Best Overall CBI Molecule 2010<br /> <br /> : '''[[Molecular Playground/CRABP I (Cellular Retinoic Acid Binding Protein)]]''', Gustavo Elberto Epalza Sanchez<br /> (compare this to the previous version above to see what's new)<br /> <br /> : **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani <br /> :: Best CBI Molecule 2012<br /> <br /> <br /> [http://people.chem.umass.edu/jhardy/ Hardy Lab]<br /> <br /> : New Fall 2012!! ''' [[Molecular Playground/Caspase-3 Regulatory Mechanisms]]''', Scott Eron, Bay Serrano, Yunlong Zhao<br /> <br /> : ''' [[Molecular Playground/Caspase-6 and neurodegeneration]]''', Kevin Buadlart Dagbay<br /> <br /> : '''[[Molecular Playground/Caspase-7 Dynamics]]'''<br /> <br /> : '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber<br /> <br /> : '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez<br /> <br /> : '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls<br /> <br /> : '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz<br /> <br /> <br /> Hebert Lab<br /> <br /> : New Fall 2012!! '''[[Molecular_Playground/ERDj5]]''', Lydia Lamriben<br /> : '''[[Molecular Playground/Saposin C]]''', Abla Tannous<br /> : '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd<br /> <br /> <br /> [http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]<br /> <br /> : '''[[Molecular_Playground/Pcr H]]''', Fabian Romano<br /> <br /> <br /> [http://people.chem.umass.edu/mholden/ Holden Lab]<br /> <br /> : New Fall 2012!! '''[[Molecular Playground/Protective Antigen]]''', Jing Huang<br /> <br /> <br /> <br /> [http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]<br /> <br /> : Updated Fall 2012!! ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski<br /> <br /> : '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita<br /> <br /> <br /> <br /> Knapp lab<br /> <br /> : Updated Fall 2012!! '''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas<br /> :: Best CBI Molecule Proteopedia Page 2010<br /> <br /> : '''[[Molecular Playground/FIH]]''', Cornelius Taabazuing, Breanne Holmes, John Hangasky<br /> <br /> <br /> [http://people.chem.umass.edu/mmaroney/ Maroney Lab]<br /> <br /> : New Fall 2012!! '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr<br /> : '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu<br /> : New Fall 2012!! '''[[Molecular Playground/HypA]]''', Heidi Hu<br /> <br /> <br /> [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> : **'''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia <br /> :: Best CBI Molecule 2011<br /> : '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia<br /> <br /> : '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan <br /> <br /> <br /> Peyton Lab<br /> : '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen<br /> : '''[[Molecular Playground/FAK]]''', Dannielle Ryman<br /> <br /> <br /> [http://roberts.openwetware.org/ Roberts Lab]<br /> <br /> : '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson<br /> <br /> : '''[[Molecular Playground/Insulin]]''', Whitney Stoppel<br /> <br /> <br /> [http://www.umass.edu/rotellogroup/ Rotello Lab]<br /> <br /> : '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino<br /> <br /> : '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang<br /> <br /> : '''[[Molecular playground/Chymotrypsin]]''', Brad<br /> <br /> : '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell<br /> <br /> <br /> <br /> [https://elements.chem.umass.edu/schnarrlab/ Schnarr Lab] <br /> <br /> : New Fall 2012!! '''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey <br /> <br /> : '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso<br /> <br /> : '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad<br /> <br /> <br /> Tew Lab<br /> <br /> : '''[[Molecular Playground/HIV Tat]]''', Brittany deRonde<br /> <br /> <br /> Thayumanavan Lab<br /> <br /> : '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez<br /> <br /> : '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura<br /> <br /> : '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi<br /> <br /> : '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy<br /> <br /> : '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado <br /> <br /> : '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang<br /> <br /> : ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo<br /> <br /> : '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko<br /> <br /> <br /> Thayumanavan & Vachet Labs<br /> <br /> : '''[[Molecular Playground/Trypsin]]''', Gladys Murage<br /> <br /> <br /> [http://people.chem.umass.edu/thompson/index.html Thompson] & [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs<br /> <br /> : New Fall 2012!! '''[[Molecular Playground/CheA]]''', Elizabeth R. Haglin<br /> <br /> : '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones<br /> <br /> : '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang<br /> <br /> : '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li<br /> <br /> <br /> [http://www.chem.umass.edu/~vachet/index.html Vachet Lab]<br /> <br /> : '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto<br /> :: Best CBI Molecule Jmol scenes 2010<br /> <br /> : '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou <br /> <br /> :'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne<br /> <br /> : New Fall 2012!! '''[[Ubiquitin salt bridge discussion]]''', Zhe Zhang<br /> <br /> <br /> Other Molecules of interest<br /> <br /> : '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> <br /> Other Laboratories<br /> <br /> : '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]<br /> <br /> : '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab<br /> <br /> : '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab<br /> <br /> ==Instructions==<br /> <br /> '''Congratulations to the prize-winning CBI molecules noted above! The new goal is for students to work collaboratively to create one excellent CBI Molecule for each CBI research group, to be featured on the CBI website.'''<br /> <br /> Fall 2012: Complete steps 1-3 by 10/10/12, in preparation for the CBI Molecule Workshop.<br /> <br /> 1. If you don't already have one, request a Proteopedia account and log in. <br /> <br /> 2. Get started working in Proteopedia by using the links at [[Help:Contents]]. Make yourself a sandbox page: Enter "User:Your Name/Sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. Practice entering text, inserting a structure window with scrolling text (green 4-square button on the right), and creating a green scene. You can look at other Proteopedia pages in edit mode to see how different effects (like colored text) are achieved (but this won't show you how the scene effects are made). <br /> <br /> 3. Get together with the other Chalk Talk students in your research group and decide which molecule you will improve or create. Develop ideas for the scenes you wish to show. You will work on these during the workshop with our help, and then finish them on your own.<br /> <br /> You are encouraged to collaborate on this year's CBI Molecules, but everyone will need to do some editing of the molecule so that they each appear as authors on the final list. If you are the sole student from your group enrolled in Chalk Talk and have not previously made a CBI Molecule, try to convince another group member who has previously made a CBI Molecule (see list above) to join us for the workshop so that you can work together.<br /> <br /> A successful CBI Molecule will be an interesting, nontechnical description of a molecule related to your group's research. It should not be super long, but instead have multiple green scenes. Green scenes should clearly show an interesting feature and should be attractive. Use the green scenes to help you make interesting points about the molecule (do not try to describe every feature of the molecule). It's great if you can end with a brief statement about how it relates to your group's research goals.<br /> <br /> 4. Your final pages should be called "Molecular Playground/your molecule" and should have links on this CBI Molecule page -- put the new ones first on the list from your research group. Label them "in progress" until you are finished.<br /> <br /> ==Links to HELP pages==<br /> Overview at [[Help:Contents ]]<br /> <br /> See also [[Help:Getting_Started_in_Proteopedia]] <br /> <br /> Videos showing how to use Proteopedia:<br /> [[Proteopedia:Video_Guide]]<br /> (Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)<br /> <br /> [[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]<br /> gives succinct step by step instructions on how to create a molecular scene.<br /> <br /> A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.<br /> [http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]<br /> <br /> [[Proteopedia:Guidelines for Ethical Writing]].<br /> Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.<br /> <br /> For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.</div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=Molecular_Playground/OmpG2&diff=1635137 Molecular Playground/OmpG2 2012-12-17T17:44:06Z

<p>Carrie Morrison Penland: New page: Protein biosensors serve as an analytical device combining a biological component with a physiochemical detector. Through protein engineering we are able to utilize pores to be used as st...</p> <hr /> <div>Protein biosensors serve as an analytical device combining a biological component with a physiochemical detector. Through protein engineering we are able to utilize pores to be used as stochastic sensors, for single molecule detection. The applications of biosensors range from fundamental research, clinical diagnosis, and even advances in homeland security. PCR (Polymerase chain reaction) and ELISA (Enzyme- linked immunosorbent assay) are current sensitive detection methods. However, these methods are time consuming and require laborious effort, where results are provided hours or days later. For this reason alternate approaches are mounting in demands that are rapid in detection time, highly sensitive and reliable. <br /> <br /> Through stochastic sensing, utilizes the passage of ionic current through a protein pore containing engineered recognition sites, allowing for monitoring of analytes present. We propose the use of monomeric protein OmpG (outer membrane protein G) will allow us to tailor and fine tune properties of this pore in detection of analytes. This monomeric porin has features, which allow for complex properties to be customized as a sensor compartment, via protein engineering, providing eminent potential for the development of this protein as a successful biosensor. Utilizing the flexibility of an extracellular loop, we will append a ligand to help detect our target analyte. <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene><br /> <br /> <br /> <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'>Opening of pore</scene><br /> <scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'>Location of ligand</scene><br /> <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene><br /> <br /> <br /> <Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'></div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=CBI_Molecules&diff=1635136 CBI Molecules 2012-12-17T17:43:28Z

<p>Carrie Morrison Penland: </p> <hr /> <div>These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].<br /> Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.<br /> <br /> UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.<br /> <br /> Fall 2012: CBI Molecules are due 12/12/12 and should be added at the TOP of the list from your lab. Label it as "in progress" until you are finished. For those editing an existing CBI Molecule, start from that entry so that it retains the full author list of all authors that contributed (or include credits to the original page and authors if it does not -- I may be able to request additions to the author list).<br /> <br /> <br /> ==Molecules==<br /> '''** Designates CBI Molecules Featured on [http://http://www.umass.edu/cbi/ CBI website]'''<br /> <br /> Bhatia Lab<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer<br /> <br /> <br /> [http://chamberslab.com/wp/ Chambers Lab]<br /> <br /> : '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano<br /> <br /> <br /> <br /> [http://www.chem.umass.edu/~chenlab/index.HTML Chen Lab]<br /> <br /> : '''[[Molecular Playground/OmpG2]]''', Christina Chisholm<br /> <br /> <br /> [http://openwetware.org/wiki/Chien Chien Lab]<br /> <br /> : **'''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau <br /> :: Best CBI Molecule 2011<br /> <br /> : '''[[Molecular Playground/DNA replication initiator DnaA]]''', Jing Liu<br /> <br /> <br /> Forbes Lab<br /> <br /> : '''[[Molecular Playground/CheR]]''', Miaomin Zhang<br /> <br /> : '''[[Molecular Playground/RBP]]''', Jan Panteli<br /> <br /> : '''[[Molecular Playground/TRAIL]]''', Charley Swofford<br /> <br /> <br /> [http://www.biochem.umass.edu/garman/index.html Garman Lab]<br /> <br /> : '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon<br /> <br /> : '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli<br /> <br /> <br /> [http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]<br /> <br /> : '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy<br /> :: Best Overall CBI Molecule 2010<br /> <br /> : '''[[Molecular Playground/CRABP I (Cellular Retinoic Acid Binding Protein)]]''', Gustavo Elberto Epalza Sanchez<br /> (compare this to the previous version above to see what's new)<br /> <br /> : **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani <br /> :: Best CBI Molecule 2012<br /> <br /> <br /> [http://people.chem.umass.edu/jhardy/ Hardy Lab]<br /> <br /> : '''[[Molecular Playground/[[Caspase-3 Regulatory Mechanisms]]''', Scott Eron, Bay Serrano, Yunlong Zhao<br /> <br /> : ''' [[Molecular Playground/Caspase-6 and neurodegeneration]]''', Kevin Buadlart Dagbay<br /> <br /> : '''[[Molecular Playground/Caspase-7 Dynamics]]'''<br /> <br /> : '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber<br /> <br /> : '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez<br /> <br /> : '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls<br /> <br /> : '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz<br /> <br /> <br /> Hebert Lab<br /> <br /> : '''[[Molecular_Playground/ERDj5]]''', Lydia Lamriben<br /> : '''[[Molecular Playground/Saposin C]]''', Abla Tannous<br /> : '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd<br /> <br /> <br /> [http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]<br /> <br /> : '''[[Molecular_Playground/Pcr H]]''', Fabian Romano<br /> <br /> <br /> [http://people.chem.umass.edu/mholden/ Holden Lab]<br /> <br /> : '''[[Molecular Playground/Protective Antigen]]''', Jing Huang<br /> <br /> <br /> <br /> [http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]<br /> <br /> : ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski<br /> <br /> : '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita<br /> <br /> <br /> <br /> Knapp lab<br /> <br /> :'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas<br /> :: Best CBI Molecule Proteopedia Page 2010<br /> <br /> : '''[[Molecular Playground/FIH]]''', Cornelius Taabazuing, Breanne Holmes, John Hangasky<br /> <br /> <br /> [http://people.chem.umass.edu/mmaroney/ Maroney Lab]<br /> <br /> : New Fall 2012!! '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr<br /> : '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu<br /> : New Fall 2012!! '''[[Molecular Playground/HypA]]''', Heidi Hu<br /> <br /> <br /> [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> : **'''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia <br /> :: Best CBI Molecule 2011<br /> : '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia<br /> <br /> : '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan <br /> <br /> <br /> Peyton Lab<br /> : '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen<br /> : '''[[Molecular Playground/FAK]]''', Dannielle Ryman<br /> <br /> <br /> [http://roberts.openwetware.org/ Roberts Lab]<br /> <br /> : '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson<br /> <br /> : '''[[Molecular Playground/Insulin]]''', Whitney Stoppel<br /> <br /> <br /> [http://www.umass.edu/rotellogroup/ Rotello Lab]<br /> <br /> : '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino<br /> <br /> : '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang<br /> <br /> : '''[[Molecular playground/Chymotrypsin]]''', Brad<br /> <br /> : '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell<br /> <br /> <br /> <br /> [https://elements.chem.umass.edu/schnarrlab/ Schnarr Lab] <br /> <br /> : '''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey <br /> <br /> : '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso<br /> <br /> : '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad<br /> <br /> <br /> Tew Lab<br /> <br /> : '''[[Molecular Playground/HIV Tat]]''', Brittany deRonde<br /> <br /> <br /> Thayumanavan Lab<br /> <br /> : '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez<br /> <br /> : '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura<br /> <br /> : '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi<br /> <br /> : '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy<br /> <br /> : '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado <br /> <br /> : '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang<br /> <br /> : ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo<br /> <br /> : '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko<br /> <br /> <br /> Thayumanavan & Vachet Labs<br /> <br /> : '''[[Molecular Playground/Trypsin]]''', Gladys Murage<br /> <br /> <br /> [http://people.chem.umass.edu/thompson/index.html Thompson] & [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs<br /> <br /> : '''[[Molecular Playground/CheA]]''', Elizabeth R. Haglin<br /> <br /> : '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones<br /> <br /> : '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang<br /> <br /> : '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li<br /> <br /> <br /> [http://www.chem.umass.edu/~vachet/index.html Vachet Lab]<br /> <br /> : '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto<br /> :: Best CBI Molecule Jmol scenes 2010<br /> <br /> : '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou <br /> <br /> :'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne<br /> <br /> <br /> <br /> Other Molecules of interest<br /> <br /> : '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> <br /> Other Laboratories<br /> <br /> : '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]<br /> <br /> : '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab<br /> <br /> : '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab<br /> <br /> ==Instructions==<br /> <br /> '''Congratulations to the prize-winning CBI molecules noted above! The new goal is for students to work collaboratively to create one excellent CBI Molecule for each CBI research group, to be featured on the CBI website.'''<br /> <br /> Fall 2012: Complete steps 1-3 by 10/10/12, in preparation for the CBI Molecule Workshop.<br /> <br /> 1. If you don't already have one, request a Proteopedia account and log in. <br /> <br /> 2. Get started working in Proteopedia by using the links at [[Help:Contents]]. Make yourself a sandbox page: Enter "User:Your Name/Sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. Practice entering text, inserting a structure window with scrolling text (green 4-square button on the right), and creating a green scene. You can look at other Proteopedia pages in edit mode to see how different effects (like colored text) are achieved (but this won't show you how the scene effects are made). <br /> <br /> 3. Get together with the other Chalk Talk students in your research group and decide which molecule you will improve or create. Develop ideas for the scenes you wish to show. You will work on these during the workshop with our help, and then finish them on your own.<br /> <br /> You are encouraged to collaborate on this year's CBI Molecules, but everyone will need to do some editing of the molecule so that they each appear as authors on the final list. If you are the sole student from your group enrolled in Chalk Talk and have not previously made a CBI Molecule, try to convince another group member who has previously made a CBI Molecule (see list above) to join us for the workshop so that you can work together.<br /> <br /> A successful CBI Molecule will be an interesting, nontechnical description of a molecule related to your group's research. It should not be super long, but instead have multiple green scenes. Green scenes should clearly show an interesting feature and should be attractive. Use the green scenes to help you make interesting points about the molecule (do not try to describe every feature of the molecule). It's great if you can end with a brief statement about how it relates to your group's research goals.<br /> <br /> 4. Your final pages should be called "Molecular Playground/your molecule" and should have links on this CBI Molecule page -- put the new ones first on the list from your research group. Label them "in progress" until you are finished.<br /> <br /> ==Links to HELP pages==<br /> Overview at [[Help:Contents ]]<br /> <br /> See also [[Help:Getting_Started_in_Proteopedia]] <br /> <br /> Videos showing how to use Proteopedia:<br /> [[Proteopedia:Video_Guide]]<br /> (Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)<br /> <br /> [[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]<br /> gives succinct step by step instructions on how to create a molecular scene.<br /> <br /> A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.<br /> [http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]<br /> <br /> [[Proteopedia:Guidelines for Ethical Writing]].<br /> Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.<br /> <br /> For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.</div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=CBI_Molecules&diff=1635007 CBI Molecules 2012-12-13T16:36:08Z

<p>Carrie Morrison Penland: </p> <hr /> <div>These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].<br /> Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.<br /> <br /> UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.<br /> <br /> Fall 2012: CBI Molecules are due 12/12/12 and should be added at the TOP of the list from your lab. Label it as "in progress" until you are finished. For those editing an existing CBI Molecule, start from that entry so that it retains the full author list of all authors that contributed (or include credits to the original page and authors if it does not -- I may be able to request additions to the author list).<br /> <br /> <br /> ==Molecules==<br /> '''** Designates CBI Molecules Featured on [http://http://www.umass.edu/cbi/ CBI website]'''<br /> <br /> Bhatia Lab<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer<br /> <br /> <br /> [http://chamberslab.com/wp/ Chambers Lab]<br /> <br /> : '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano<br /> <br /> <br /> <br /> [http://www.chem.umass.edu/~chenlab/index.HTML Chen Lab]<br /> <br /> <br /> <br /> [http://openwetware.org/wiki/Chien Chien Lab]<br /> <br /> : **'''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau <br /> :: Best CBI Molecule 2011<br /> <br /> : '''[[Molecular Playground/DNA replication initiator DnaA]]''', Jing Liu<br /> <br /> <br /> Forbes Lab<br /> <br /> : '''[[Molecular Playground/CheR]]''', Miaomin Zhang<br /> <br /> : '''[[Molecular Playground/RBP]]''', Jan Panteli<br /> <br /> : '''[[Molecular Playground/TRAIL]]''', Charley Swofford<br /> <br /> <br /> [http://www.biochem.umass.edu/garman/index.html Garman Lab]<br /> <br /> : '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon<br /> <br /> : '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli<br /> <br /> <br /> [http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]<br /> <br /> : '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy<br /> :: Best Overall CBI Molecule 2010<br /> <br /> : '''[[Molecular Playground/CRABP I (Cellular Retinoic Acid Binding Protein)]]''', Gustavo Elberto Epalza Sanchez<br /> (compare this to the previous version above to see what's new)<br /> <br /> : **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani <br /> :: Best CBI Molecule 2012<br /> <br /> <br /> [http://people.chem.umass.edu/jhardy/ Hardy Lab]<br /> <br /> : '''[[Molecular Playground/[[Caspase-3 Regulatory Mechanisms]]''', Scott Eron, Bay Serrano, Yunlong Zhao<br /> <br /> : ''' [[Molecular Playground/Caspase-6 and neurodegeneration]]''', Kevin Buadlart Dagbay<br /> <br /> : '''[[Molecular Playground/Caspase-7 Dynamics]]'''<br /> <br /> : '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber<br /> <br /> : '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez<br /> <br /> : '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls<br /> <br /> : '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz<br /> <br /> <br /> Hebert Lab<br /> <br /> : '''[[Molecular_Playground/ERDj5]]''', Lydia Lamriben<br /> : '''[[Molecular Playground/Saposin C]]''', Abla Tannous<br /> : '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd<br /> <br /> <br /> [http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]<br /> <br /> : '''[[Molecular_Playground/Pcr H]]''', Fabian Romano<br /> <br /> <br /> [http://people.chem.umass.edu/mholden/ Holden Lab]<br /> <br /> <br /> <br /> [http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]<br /> <br /> : ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski<br /> <br /> : '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita<br /> <br /> <br /> <br /> Knapp lab<br /> <br /> :'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas<br /> :: Best CBI Molecule Proteopedia Page 2010<br /> <br /> : '''[[Molecular Playground/FIH]]''', Cornelius Taabazuing, Breanne Holmes, John Hangasky<br /> <br /> <br /> [http://people.chem.umass.edu/mmaroney/ Maroney Lab]<br /> <br /> : New Fall 2012!! '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr<br /> : '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu<br /> : New Fall 2012!! '''[[Molecular Playground/HypA]]''', Heidi Hu<br /> <br /> <br /> [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> : **'''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia <br /> :: Best CBI Molecule 2011<br /> : '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia<br /> <br /> : '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan <br /> <br /> <br /> Peyton Lab<br /> : '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen<br /> : '''[[Molecular Playground/FAK]]''', Dannielle Ryman<br /> <br /> <br /> [http://roberts.openwetware.org/ Roberts Lab]<br /> <br /> : '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson<br /> <br /> : '''[[Molecular Playground/Insulin]]''', Whitney Stoppel<br /> <br /> <br /> [http://www.umass.edu/rotellogroup/ Rotello Lab]<br /> <br /> : '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino<br /> <br /> : '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang<br /> <br /> : '''[[Molecular playground/Chymotrypsin]]''', Brad<br /> <br /> : '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell<br /> <br /> <br /> <br /> [https://elements.chem.umass.edu/schnarrlab/ Schnarr Lab] <br /> <br /> : '''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey <br /> <br /> : '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso<br /> <br /> : '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad<br /> <br /> <br /> Tew Lab<br /> <br /> : '''[[Molecular Playground/HIV Tat]]''', Brittany deRonde<br /> <br /> <br /> Thayumanavan Lab<br /> <br /> : '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez<br /> <br /> : '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura<br /> <br /> : '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi<br /> <br /> : '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy<br /> <br /> : '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado <br /> <br /> : '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang<br /> <br /> : ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo<br /> <br /> : '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko<br /> <br /> <br /> Thayumanavan & Vachet Labs<br /> <br /> : '''[[Molecular Playground/Trypsin]]''', Gladys Murage<br /> <br /> <br /> [http://people.chem.umass.edu/thompson/index.html Thompson] & [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs<br /> <br /> : '''[[Molecular Playground/CheA]]''', Elizabeth R. Haglin<br /> <br /> : '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones<br /> <br /> : '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang<br /> <br /> : '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li<br /> <br /> <br /> [http://www.chem.umass.edu/~vachet/index.html Vachet Lab]<br /> <br /> : '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto<br /> :: Best CBI Molecule Jmol scenes 2010<br /> <br /> : '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou <br /> <br /> :'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne<br /> <br /> <br /> <br /> Other Molecules of interest<br /> <br /> : '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> <br /> Other Laboratories<br /> <br /> : '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]<br /> <br /> : '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab<br /> <br /> : '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab<br /> <br /> ==Instructions==<br /> <br /> '''Congratulations to the prize-winning CBI molecules noted above! The new goal is for students to work collaboratively to create one excellent CBI Molecule for each CBI research group, to be featured on the CBI website.'''<br /> <br /> Fall 2012: Complete steps 1-3 by 10/10/12, in preparation for the CBI Molecule Workshop.<br /> <br /> 1. If you don't already have one, request a Proteopedia account and log in. <br /> <br /> 2. Get started working in Proteopedia by using the links at [[Help:Contents]]. Make yourself a sandbox page: Enter "User:Your Name/Sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. Practice entering text, inserting a structure window with scrolling text (green 4-square button on the right), and creating a green scene. You can look at other Proteopedia pages in edit mode to see how different effects (like colored text) are achieved (but this won't show you how the scene effects are made). <br /> <br /> 3. Get together with the other Chalk Talk students in your research group and decide which molecule you will improve or create. Develop ideas for the scenes you wish to show. You will work on these during the workshop with our help, and then finish them on your own.<br /> <br /> You are encouraged to collaborate on this year's CBI Molecules, but everyone will need to do some editing of the molecule so that they each appear as authors on the final list. If you are the sole student from your group enrolled in Chalk Talk and have not previously made a CBI Molecule, try to convince another group member who has previously made a CBI Molecule (see list above) to join us for the workshop so that you can work together.<br /> <br /> A successful CBI Molecule will be an interesting, nontechnical description of a molecule related to your group's research. It should not be super long, but instead have multiple green scenes. Green scenes should clearly show an interesting feature and should be attractive. Use the green scenes to help you make interesting points about the molecule (do not try to describe every feature of the molecule). It's great if you can end with a brief statement about how it relates to your group's research goals.<br /> <br /> 4. Your final pages should be called "Molecular Playground/your molecule" and should have links on this CBI Molecule page -- put the new ones first on the list from your research group. Label them "in progress" until you are finished.<br /> <br /> ==Links to HELP pages==<br /> Overview at [[Help:Contents ]]<br /> <br /> See also [[Help:Getting_Started_in_Proteopedia]] <br /> <br /> Videos showing how to use Proteopedia:<br /> [[Proteopedia:Video_Guide]]<br /> (Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)<br /> <br /> [[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]<br /> gives succinct step by step instructions on how to create a molecular scene.<br /> <br /> A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.<br /> [http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]<br /> <br /> [[Proteopedia:Guidelines for Ethical Writing]].<br /> Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.<br /> <br /> For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.</div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=CBI_Molecules&diff=1635006 CBI Molecules 2012-12-13T16:21:09Z

<p>Carrie Morrison Penland: </p> <hr /> <div>These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].<br /> Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.<br /> <br /> UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.<br /> <br /> Fall 2012: CBI Molecules are due 12/12/12 and should be added at the TOP of the list from your lab. Label it as "in progress" until you are finished. For those editing an existing CBI Molecule, start from that entry so that it retains the full author list of all authors that contributed (or include credits to the original page and authors if it does not -- I may be able to request additions to the author list).<br /> <br /> <br /> ==Molecules==<br /> '''** Designates CBI Molecules Featured on [http://http://www.umass.edu/cbi/ CBI website]'''<br /> <br /> Bhatia Lab<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer<br /> <br /> <br /> [http://chamberslab.com/wp/ Chambers Lab]<br /> <br /> : '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano<br /> <br /> <br /> [http://openwetware.org/wiki/Chien Chien Lab]<br /> <br /> : **'''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau <br /> :: Best CBI Molecule 2011<br /> <br /> : '''[[Molecular Playground/DNA replication initiator DnaA]]''', Jing Liu<br /> <br /> <br /> Forbes Lab<br /> <br /> : '''[[Molecular Playground/CheR]]''', Miaomin Zhang<br /> <br /> : '''[[Molecular Playground/RBP]]''', Jan Panteli<br /> <br /> : '''[[Molecular Playground/TRAIL]]''', Charley Swofford<br /> <br /> <br /> [http://www.biochem.umass.edu/garman/index.html Garman Lab]<br /> <br /> : '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon<br /> <br /> : '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli<br /> <br /> <br /> [http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]<br /> <br /> : '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy<br /> :: Best Overall CBI Molecule 2010<br /> <br /> : '''[[Molecular Playground/CRABP I (Cellular Retinoic Acid Binding Protein)]]''', Gustavo Elberto Epalza Sanchez<br /> (compare this to the previous version above to see what's new)<br /> <br /> : **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani <br /> :: Best CBI Molecule 2012<br /> <br /> <br /> [http://people.chem.umass.edu/jhardy/ Hardy Lab]<br /> <br /> : '''[[Molecular Playground/[[Caspase-3 Regulatory Mechanisms]]''', Scott Eron, Bay Serrano, Yunlong Zhao<br /> <br /> : ''' [[Molecular Playground/Caspase-6 and neurodegeneration]]''', Kevin Buadlart Dagbay<br /> <br /> : '''[[Molecular Playground/Caspase-7 Dynamics]]'''<br /> <br /> : '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber<br /> <br /> : '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez<br /> <br /> : '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls<br /> <br /> : '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz<br /> <br /> <br /> Hebert Lab<br /> <br /> : '''[[Molecular_Playground/ERDj5]]''', Lydia Lamriben<br /> : '''[[Molecular Playground/Saposin C]]''', Abla Tannous<br /> : '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd<br /> <br /> <br /> [http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]<br /> <br /> : '''[[Molecular_Playground/Pcr H]]''', Fabian Romano<br /> <br /> <br /> [http://people.chem.umass.edu/mholden/ Holden Lab]<br /> <br /> <br /> <br /> [http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]<br /> <br /> : ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski<br /> <br /> : '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita<br /> <br /> <br /> <br /> Knapp lab<br /> <br /> :'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas<br /> :: Best CBI Molecule Proteopedia Page 2010<br /> <br /> : '''[[Molecular Playground/FIH]]''', Cornelius Taabazuing, Breanne Holmes, John Hangasky<br /> <br /> <br /> [http://people.chem.umass.edu/mmaroney/ Maroney Lab]<br /> <br /> : New Fall 2012!! '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr<br /> : '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu<br /> : New Fall 2012!! '''[[Molecular Playground/HypA]]''', Heidi Hu<br /> <br /> <br /> [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> : **'''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia <br /> :: Best CBI Molecule 2011<br /> : '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia<br /> <br /> : '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan <br /> <br /> <br /> Peyton Lab<br /> : '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen<br /> : '''[[Molecular Playground/FAK]]''', Dannielle Ryman<br /> <br /> <br /> [http://roberts.openwetware.org/ Roberts Lab]<br /> <br /> : '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson<br /> <br /> : '''[[Molecular Playground/Insulin]]''', Whitney Stoppel<br /> <br /> <br /> [http://www.umass.edu/rotellogroup/ Rotello Lab]<br /> <br /> : '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino<br /> <br /> : '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang<br /> <br /> : '''[[Molecular playground/Chymotrypsin]]''', Brad<br /> <br /> : '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell<br /> <br /> <br /> <br /> [https://elements.chem.umass.edu/schnarrlab/ Schnarr Lab] <br /> <br /> : '''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey <br /> <br /> : '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso<br /> <br /> : '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad<br /> <br /> <br /> Tew Lab<br /> <br /> : '''[[Molecular Playground/HIV Tat]]''', Brittany deRonde<br /> <br /> <br /> Thayumanavan Lab<br /> <br /> : '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez<br /> <br /> : '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura<br /> <br /> : '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi<br /> <br /> : '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy<br /> <br /> : '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado <br /> <br /> : '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang<br /> <br /> : ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo<br /> <br /> : '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko<br /> <br /> <br /> Thayumanavan & Vachet Labs<br /> <br /> : '''[[Molecular Playground/Trypsin]]''', Gladys Murage<br /> <br /> <br /> [http://people.chem.umass.edu/thompson/index.html Thompson] & [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs<br /> <br /> : '''[[Molecular Playground/CheA]]''', Elizabeth R. Haglin<br /> <br /> : '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones<br /> <br /> : '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang<br /> <br /> : '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li<br /> <br /> <br /> [http://www.chem.umass.edu/~vachet/index.html Vachet Lab]<br /> <br /> : '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto<br /> :: Best CBI Molecule Jmol scenes 2010<br /> <br /> : '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou <br /> <br /> :'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne<br /> <br /> <br /> <br /> Other Molecules of interest<br /> <br /> : '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> <br /> Other Laboratories<br /> <br /> : '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]<br /> <br /> : '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab<br /> <br /> : '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab<br /> <br /> ==Instructions==<br /> <br /> '''Congratulations to the prize-winning CBI molecules noted above! The new goal is for students to work collaboratively to create one excellent CBI Molecule for each CBI research group, to be featured on the CBI website.'''<br /> <br /> Fall 2012: Complete steps 1-3 by 10/10/12, in preparation for the CBI Molecule Workshop.<br /> <br /> 1. If you don't already have one, request a Proteopedia account and log in. <br /> <br /> 2. Get started working in Proteopedia by using the links at [[Help:Contents]]. Make yourself a sandbox page: Enter "User:Your Name/Sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. Practice entering text, inserting a structure window with scrolling text (green 4-square button on the right), and creating a green scene. You can look at other Proteopedia pages in edit mode to see how different effects (like colored text) are achieved (but this won't show you how the scene effects are made). <br /> <br /> 3. Get together with the other Chalk Talk students in your research group and decide which molecule you will improve or create. Develop ideas for the scenes you wish to show. You will work on these during the workshop with our help, and then finish them on your own.<br /> <br /> You are encouraged to collaborate on this year's CBI Molecules, but everyone will need to do some editing of the molecule so that they each appear as authors on the final list. If you are the sole student from your group enrolled in Chalk Talk and have not previously made a CBI Molecule, try to convince another group member who has previously made a CBI Molecule (see list above) to join us for the workshop so that you can work together.<br /> <br /> A successful CBI Molecule will be an interesting, nontechnical description of a molecule related to your group's research. It should not be super long, but instead have multiple green scenes. Green scenes should clearly show an interesting feature and should be attractive. Use the green scenes to help you make interesting points about the molecule (do not try to describe every feature of the molecule). It's great if you can end with a brief statement about how it relates to your group's research goals.<br /> <br /> 4. Your final pages should be called "Molecular Playground/your molecule" and should have links on this CBI Molecule page -- put the new ones first on the list from your research group. Label them "in progress" until you are finished.<br /> <br /> ==Links to HELP pages==<br /> Overview at [[Help:Contents ]]<br /> <br /> See also [[Help:Getting_Started_in_Proteopedia]] <br /> <br /> Videos showing how to use Proteopedia:<br /> [[Proteopedia:Video_Guide]]<br /> (Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)<br /> <br /> [[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]<br /> gives succinct step by step instructions on how to create a molecular scene.<br /> <br /> A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.<br /> [http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]<br /> <br /> [[Proteopedia:Guidelines for Ethical Writing]].<br /> Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.<br /> <br /> For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.</div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=CBI_Molecules&diff=1635005 CBI Molecules 2012-12-13T16:20:18Z

<p>Carrie Morrison Penland: </p> <hr /> <div>These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].<br /> Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.<br /> <br /> UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.<br /> <br /> Fall 2012: CBI Molecules are due 12/12/12 and should be added at the TOP of the list from your lab. Label it as "in progress" until you are finished. For those editing an existing CBI Molecule, start from that entry so that it retains the full author list of all authors that contributed (or include credits to the original page and authors if it does not -- I may be able to request additions to the author list).<br /> <br /> <br /> ==Molecules==<br /> '''** Designates CBI Molecules Featured on [http://http://www.umass.edu/cbi/ CBI website]'''<br /> <br /> Bhatia Lab<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer<br /> <br /> <br /> [http://chamberslab.com/wp/ Chambers Lab]<br /> <br /> : '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano<br /> <br /> <br /> [http://openwetware.org/wiki/Chien Chien Lab]<br /> <br /> : **'''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau <br /> :: Best CBI Molecule 2011<br /> <br /> : '''[[Molecular Playground/DNA replication initiator DnaA]]''', Jing Liu<br /> <br /> <br /> Forbes Lab<br /> <br /> : '''[[Molecular Playground/CheR]]''', Miaomin Zhang<br /> <br /> : '''[[Molecular Playground/RBP]]''', Jan Panteli<br /> <br /> : '''[[Molecular Playground/TRAIL]]''', Charley Swofford<br /> <br /> <br /> [http://www.biochem.umass.edu/garman/index.html Garman Lab]<br /> <br /> : '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon<br /> <br /> : '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli<br /> <br /> <br /> [http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]<br /> <br /> : '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy<br /> :: Best Overall CBI Molecule 2010<br /> <br /> : '''[[Molecular Playground/CRABP I (Cellular Retinoic Acid Binding Protein)]]''', Gustavo Elberto Epalza Sanchez<br /> (compare this to the previous version above to see what's new)<br /> <br /> : **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani <br /> :: Best CBI Molecule 2012<br /> <br /> <br /> [http://people.chem.umass.edu/jhardy/ Hardy Lab]<br /> <br /> : '''[[Molecular Playground/[[Caspase-3 Regulatory Mechanisms]]''', Scott Eron, Bay Serrano, Yunlong Zhao<br /> <br /> : ''' [[Molecular Playground/Caspase-6 and neurodegeneration]]''', Kevin Buadlart Dagbay<br /> <br /> : '''[[Molecular Playground/Caspase-7 Dynamics]]'''<br /> <br /> : '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber<br /> <br /> : '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez<br /> <br /> : '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls<br /> <br /> : '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz<br /> <br /> <br /> Hebert Lab<br /> <br /> : '''[[Molecular_Playground/ERDj5]]''', Lydia Lamriben<br /> : '''[[Molecular Playground/Saposin C]]''', Abla Tannous<br /> : '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd<br /> <br /> <br /> [http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]<br /> <br /> : '''[[Molecular_Playground/Pcr H]]''', Fabian Romano<br /> <br /> <br /> [http://people.chem.umass.edu/mholden/ Holden Lab]<br /> <br /> <br /> <br /> [http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]<br /> <br /> : ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski<br /> <br /> : '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita<br /> <br /> <br /> <br /> Knapp lab<br /> <br /> :'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas<br /> :: Best CBI Molecule Proteopedia Page 2010<br /> <br /> : '''[[Molecular Playground/FIH]]''', Cornelius Taabazuing, Breanne Holmes, John Hangasky<br /> <br /> <br /> [http://people.chem.umass.edu/mmaroney/ Maroney Lab]<br /> <br /> : New Fall 2012!! '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr<br /> : '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu<br /> : New Fall 2012!! '''[[Molecular Playground/HypA]]''', Heidi Hu<br /> <br /> <br /> [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> : **'''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia <br /> :: Best CBI Molecule 2011<br /> : '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia<br /> <br /> : '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan <br /> <br /> <br /> Peyton Lab<br /> : '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen<br /> : '''[[Molecular Playground/FAK]]''', Dannielle Ryman<br /> <br /> <br /> [http://roberts.openwetware.org/ Roberts Lab]<br /> <br /> : '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson<br /> <br /> : '''[[Molecular Playground/Insulin]]''', Whitney Stoppel<br /> <br /> <br /> [http://www.umass.edu/rotellogroup/ Rotello Lab]<br /> <br /> : '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino<br /> <br /> : '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang<br /> <br /> : '''[[Molecular playground/Chymotrypsin]]''', Brad<br /> <br /> : '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell<br /> <br /> <br /> <br /> [https://elements.chem.umass.edu/schnarrlab/ Schnarr Lab ] <br /> <br /> : '''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey <br /> <br /> : '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso<br /> <br /> : '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad<br /> <br /> <br /> Tew Lab<br /> <br /> : '''[[Molecular Playground/HIV Tat]]''', Brittany deRonde<br /> <br /> <br /> Thayumanavan Lab<br /> <br /> : '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez<br /> <br /> : '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura<br /> <br /> : '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi<br /> <br /> : '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy<br /> <br /> : '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado <br /> <br /> : '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang<br /> <br /> : ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo<br /> <br /> : '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko<br /> <br /> <br /> Thayumanavan & Vachet Labs<br /> <br /> : '''[[Molecular Playground/Trypsin]]''', Gladys Murage<br /> <br /> <br /> [http://people.chem.umass.edu/thompson/index.html Thompson] & [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs<br /> <br /> : '''[[Molecular Playground/CheA]]''', Elizabeth R. Haglin<br /> <br /> : '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones<br /> <br /> : '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang<br /> <br /> : '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li<br /> <br /> <br /> [http://www.chem.umass.edu/~vachet/index.html Vachet Lab]<br /> <br /> : '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto<br /> :: Best CBI Molecule Jmol scenes 2010<br /> <br /> : '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou <br /> <br /> :'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne<br /> <br /> <br /> <br /> Other Molecules of interest<br /> <br /> : '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> <br /> Other Laboratories<br /> <br /> : '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]<br /> <br /> : '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab<br /> <br /> : '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab<br /> <br /> ==Instructions==<br /> <br /> '''Congratulations to the prize-winning CBI molecules noted above! The new goal is for students to work collaboratively to create one excellent CBI Molecule for each CBI research group, to be featured on the CBI website.'''<br /> <br /> Fall 2012: Complete steps 1-3 by 10/10/12, in preparation for the CBI Molecule Workshop.<br /> <br /> 1. If you don't already have one, request a Proteopedia account and log in. <br /> <br /> 2. Get started working in Proteopedia by using the links at [[Help:Contents]]. Make yourself a sandbox page: Enter "User:Your Name/Sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. Practice entering text, inserting a structure window with scrolling text (green 4-square button on the right), and creating a green scene. You can look at other Proteopedia pages in edit mode to see how different effects (like colored text) are achieved (but this won't show you how the scene effects are made). <br /> <br /> 3. Get together with the other Chalk Talk students in your research group and decide which molecule you will improve or create. Develop ideas for the scenes you wish to show. You will work on these during the workshop with our help, and then finish them on your own.<br /> <br /> You are encouraged to collaborate on this year's CBI Molecules, but everyone will need to do some editing of the molecule so that they each appear as authors on the final list. If you are the sole student from your group enrolled in Chalk Talk and have not previously made a CBI Molecule, try to convince another group member who has previously made a CBI Molecule (see list above) to join us for the workshop so that you can work together.<br /> <br /> A successful CBI Molecule will be an interesting, nontechnical description of a molecule related to your group's research. It should not be super long, but instead have multiple green scenes. Green scenes should clearly show an interesting feature and should be attractive. Use the green scenes to help you make interesting points about the molecule (do not try to describe every feature of the molecule). It's great if you can end with a brief statement about how it relates to your group's research goals.<br /> <br /> 4. Your final pages should be called "Molecular Playground/your molecule" and should have links on this CBI Molecule page -- put the new ones first on the list from your research group. Label them "in progress" until you are finished.<br /> <br /> ==Links to HELP pages==<br /> Overview at [[Help:Contents ]]<br /> <br /> See also [[Help:Getting_Started_in_Proteopedia]] <br /> <br /> Videos showing how to use Proteopedia:<br /> [[Proteopedia:Video_Guide]]<br /> (Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)<br /> <br /> [[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]<br /> gives succinct step by step instructions on how to create a molecular scene.<br /> <br /> A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.<br /> [http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]<br /> <br /> [[Proteopedia:Guidelines for Ethical Writing]].<br /> Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.<br /> <br /> For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.</div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=CBI_Molecules&diff=1632856 CBI Molecules 2012-12-12T21:27:08Z

<p>Carrie Morrison Penland: </p> <hr /> <div>These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].<br /> Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.<br /> <br /> UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.<br /> <br /> Fall 2012: CBI Molecules are due 12/12/12 and should be added at the TOP of the list from your lab. Label it as "in progress" until you are finished. For those editing an existing CBI Molecule, start from that entry so that it retains the full author list of all authors that contributed (or include credits to the original page and authors if it does not -- I may be able to request additions to the author list).<br /> <br /> <br /> ==Molecules==<br /> '''** Designates CBI Molecules Featured on [http://http://www.umass.edu/cbi/ CBI website]'''<br /> <br /> Bhatia Lab<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer<br /> <br /> <br /> [http://chamberslab.com/wp/ Chambers Lab]<br /> <br /> : '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano<br /> <br /> <br /> [http://openwetware.org/wiki/Chien Chien Lab]<br /> <br /> : **'''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau <br /> :: Best CBI Molecule 2011<br /> <br /> : '''[[Molecular Playground/DNA replication initiator DnaA]]''', Jing Liu<br /> <br /> <br /> Forbes Lab<br /> <br /> : '''[[Molecular Playground/CheR]]''', Miaomin Zhang<br /> <br /> : '''[[Molecular Playground/RBP]]''', Jan Panteli<br /> <br /> : '''[[Molecular Playground/TRAIL]]''', Charley Swofford<br /> <br /> <br /> [http://www.biochem.umass.edu/garman/index.html Garman Lab]<br /> <br /> : '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon<br /> <br /> : '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli<br /> <br /> <br /> [http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]<br /> <br /> : '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy<br /> :: Best Overall CBI Molecule 2010<br /> <br /> : '''[[Molecular Playground/CRABP I (Cellular Retinoic Acid Binding Protein)]]''', Gustavo Elberto Epalza Sanchez<br /> (compare this to the previous version above to see what's new)<br /> <br /> : **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani <br /> :: Best CBI Molecule 2012<br /> <br /> <br /> [http://people.chem.umass.edu/jhardy/ Hardy Lab]<br /> <br /> : ''' [[Molecular Playground/Caspase-6 and neurodegeneration]]''', Kevin Buadlart Dagbay<br /> <br /> : '''[[Molecular Playground/Caspase-7 Dynamics]]'''<br /> <br /> : '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber<br /> <br /> : '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez<br /> <br /> : '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls<br /> <br /> : '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz<br /> <br /> <br /> Hebert Lab<br /> <br /> : '''[[Molecular Playground/Saposin C]]''', Abla Tannous<br /> : '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd<br /> <br /> <br /> [http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]<br /> <br /> : '''[[Molecular_Playground/Pcr H]]''', Fabian Romano<br /> <br /> <br /> [http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]<br /> <br /> : ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin<br /> <br /> : '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita<br /> <br /> <br /> <br /> Knapp lab<br /> <br /> :'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas<br /> :: Best CBI Molecule Proteopedia Page 2010<br /> <br /> : '''[[Molecular Playground/FIH]]''', Cornelius Taabazuing, Breanne Holmes, John Hangasky<br /> <br /> <br /> [http://people.chem.umass.edu/mmaroney/ Maroney Lab]<br /> <br /> : '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr<br /> : '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu<br /> <br /> <br /> [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> : **'''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia <br /> :: Best CBI Molecule 2011<br /> : '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia<br /> <br /> : '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan <br /> <br /> <br /> Peyton Lab<br /> : '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen<br /> : '''[[Molecular Playground/FAK]]''', Dannielle Ryman<br /> <br /> <br /> [http://roberts.openwetware.org/ Roberts Lab]<br /> <br /> : '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson<br /> <br /> : '''[[Molecular Playground/Insulin]]''', Whitney Stoppel<br /> <br /> <br /> [http://www.umass.edu/rotellogroup/ Rotello Lab]<br /> <br /> : '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino<br /> <br /> : '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang<br /> <br /> : '''[[Molecular playground/Chymotrypsin]]''', Brad<br /> <br /> : '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell<br /> <br /> <br /> Schnarr Lab <br /> <br /> : '''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey <br /> <br /> : '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso<br /> <br /> : '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad<br /> <br /> <br /> Tew Lab<br /> <br /> : '''[[Molecular Playground/HIV Tat]]''', Brittany deRonde<br /> <br /> <br /> Thayumanavan Lab<br /> <br /> : '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez<br /> <br /> : '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura<br /> <br /> : '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi<br /> <br /> : '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy<br /> <br /> : '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado <br /> <br /> : '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang<br /> <br /> : ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo<br /> <br /> : '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko<br /> <br /> <br /> Thayumanavan & Vachet Labs<br /> <br /> : '''[[Molecular Playground/Trypsin]]''', Gladys Murage<br /> <br /> <br /> [http://people.chem.umass.edu/thompson/index.html Thompson] & [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs<br /> <br /> : '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones<br /> <br /> : '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang<br /> <br /> : '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li<br /> <br /> <br /> [http://www.chem.umass.edu/~vachet/index.html Vachet Lab]<br /> <br /> : '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto<br /> :: Best CBI Molecule Jmol scenes 2010<br /> <br /> : '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou <br /> <br /> :'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne<br /> <br /> <br /> <br /> Other Molecules of interest<br /> <br /> : '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> <br /> Other Laboratories<br /> <br /> : '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]<br /> <br /> : '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab<br /> <br /> : '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab<br /> <br /> ==Instructions==<br /> <br /> '''Congratulations to the prize-winning CBI molecules noted above! The new goal is for students to work collaboratively to create one excellent CBI Molecule for each CBI research group, to be featured on the CBI website.'''<br /> <br /> Fall 2012: Complete steps 1-3 by 10/10/12, in preparation for the CBI Molecule Workshop.<br /> <br /> 1. If you don't already have one, request a Proteopedia account and log in. <br /> <br /> 2. Get started working in Proteopedia by using the links at [[Help:Contents]]. Make yourself a sandbox page: Enter "User:Your Name/Sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. Practice entering text, inserting a structure window with scrolling text (green 4-square button on the right), and creating a green scene. You can look at other Proteopedia pages in edit mode to see how different effects (like colored text) are achieved (but this won't show you how the scene effects are made). <br /> <br /> 3. Get together with the other Chalk Talk students in your research group and decide which molecule you will improve or create. Develop ideas for the scenes you wish to show. You will work on these during the workshop with our help, and then finish them on your own.<br /> <br /> You are encouraged to collaborate on this year's CBI Molecules, but everyone will need to do some editing of the molecule so that they each appear as authors on the final list. If you are the sole student from your group enrolled in Chalk Talk and have not previously made a CBI Molecule, try to convince another group member who has previously made a CBI Molecule (see list above) to join us for the workshop so that you can work together.<br /> <br /> A successful CBI Molecule will be an interesting, nontechnical description of a molecule related to your group's research. It should not be super long, but instead have multiple green scenes. Green scenes should clearly show an interesting feature and should be attractive. Use the green scenes to help you make interesting points about the molecule (do not try to describe every feature of the molecule). It's great if you can end with a brief statement about how it relates to your group's research goals.<br /> <br /> 4. Your final pages should be called "Molecular Playground/your molecule" and should have links on this CBI Molecule page -- put the new ones first on the list from your research group. Label them "in progress" until you are finished.<br /> <br /> ==Links to HELP pages==<br /> Overview at [[Help:Contents ]]<br /> <br /> See also [[Help:Getting_Started_in_Proteopedia]] <br /> <br /> Videos showing how to use Proteopedia:<br /> [[Proteopedia:Video_Guide]]<br /> (Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)<br /> <br /> [[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]<br /> gives succinct step by step instructions on how to create a molecular scene.<br /> <br /> A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.<br /> [http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]<br /> <br /> [[Proteopedia:Guidelines for Ethical Writing]].<br /> Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.<br /> <br /> For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.</div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=Sfp&diff=1632632 Sfp 2012-12-12T21:22:26Z

<p>Carrie Morrison Penland: Sfp moved to Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp): make public</p> <hr /> <div>#REDIRECT [[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]</div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=Molecular_Playground/4%27-PHOSPHOPANTETHEINYL_TRANSFERASE_(Sfp)&diff=1632631 Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp) 2012-12-12T21:22:26Z

<p>Carrie Morrison Penland: Sfp moved to Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp): make public</p> <hr /> <div>== 4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp) ==<br /> <StructureSection load='1qr0' size='350' side='right' caption='Structure of HMG-CoA reductase (PDB entry [[1dq8]])' scene=''><br /> <br /> == Introduction ==<br /> <br /> '''Sfp''' is a 4'-phosphopantetheinyl (PPant) transferase endogenous to ''B. Subtilis'', first crystallized in 1999 [1]. The function of Sfp is to transfer a phosphopantetheinyl group from <scene name='Sfp/Coa_highlight/5'>coenzyme-A</scene> (CoA-SH) to the serine residue of peptides containing the sequence "DSL". Frequently this sequence is found in acyl- or peptidyl-carrier proteins in fatty acid synthases (FASs), polyketide synthases (PKSs), and nonribosomal peptide synthetases (NRPSs). This posttranslational modification converts the inactive apo form peptide to the active holo form. The terminal thiol PPant prosthetic group acts as a point of covalent attachment between the peptide and the growing fatty acid, polyketide, or nonribosomal peptide.<br /> <br /> <br /> == Mechanism of Transfer ==<br /> <scene name='Sfp/Sfp_mg/6'>Active site magnesium</scene> along with ATP are involved in the catalytic transformation of the apo proteins.<br /> <br /> <br /> <br /> <br /> == Biochemical Applications ==<br /> <br /> <br /> <br /> </StructureSection></div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=User:Carrie_Morrison_Penland/Sandbox_3&diff=1057757 User:Carrie Morrison Penland/Sandbox 3 2010-03-17T16:05:24Z

<p>Carrie Morrison Penland: </p> <hr /> <div><applet size='[450,338]' frame='true' align='right'<br /> caption='YYY' /><br /> <scene name='User:Carrie_Morrison_Penland/Sandbox_3/3eml/1'>original</scene><br /> <br /> <scene name='User:Carrie_Morrison_Penland/Sandbox_3/3eml/2'>edited</scene></div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=User:Carrie_Morrison_Penland/Sandbox_3&diff=1057755 User:Carrie Morrison Penland/Sandbox 3 2010-03-17T15:54:41Z

<p>Carrie Morrison Penland: </p> <hr /> <div><applet size='[450,338]' frame='true' align='right'<br /> caption='YYY' /><br /> <scene name='User:Carrie_Morrison_Penland/Sandbox_3/3eml/1'>original</scene></div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=User:Carrie_Morrison_Penland/Sandbox_3&diff=1057754 User:Carrie Morrison Penland/Sandbox 3 2010-03-17T15:26:23Z

<p>Carrie Morrison Penland: </p> <hr /> <div><applet size='[450,338]' frame='true' align='right'<br /> caption='YYY' /><br /> <scene name='User:Carrie_Morrison_Penland/Sandbox_3/3eml/1'>TextToBeDisplayed</scene></div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=User:Carrie_Morrison_Penland/Sandbox_3&diff=1057750 User:Carrie Morrison Penland/Sandbox 3 2010-03-17T15:02:07Z

<p>Carrie Morrison Penland: </p> <hr /> <div><applet size='[450,338]' frame='true' align='right'<br /> caption='YYY' /></div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=Carrie_Morrison_Penland/Sandbox_3&diff=1057746 Carrie Morrison Penland/Sandbox 3 2010-03-17T14:58:52Z

<p>Carrie Morrison Penland: Carrie Morrison Penland/Sandbox 3 moved to User:Carrie Morrison Penland/Sandbox 3</p> <hr /> <div>#REDIRECT [[User:Carrie Morrison Penland/Sandbox 3]]</div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=User:Carrie_Morrison_Penland/Sandbox_3&diff=1057745 User:Carrie Morrison Penland/Sandbox 3 2010-03-17T14:58:52Z

<p>Carrie Morrison Penland: Carrie Morrison Penland/Sandbox 3 moved to User:Carrie Morrison Penland/Sandbox 3</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_3cin | PDB=3cin | SCENE= }}</div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=User:Carrie_Morrison_Penland/Sandbox_3&diff=1057744 User:Carrie Morrison Penland/Sandbox 3 2010-03-17T14:58:37Z

<p>Carrie Morrison Penland: 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_3cin | PDB=3cin | SCENE= }}</div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=Carrie_Morrison_Penland/Sandbox_1&diff=1057739 Carrie Morrison Penland/Sandbox 1 2010-03-17T14:40:21Z

<p>Carrie Morrison Penland: </p> <hr /> <div><applet size='[450,338]' frame='true' align='right'<br /> caption='YYY' /><br /> <scene name='User:Carrie_Morrison_Penland/Sandbox_1/1/1'>TextToBeDisplayed</scene><br /> <br /> <scene name='Carrie_Morrison_Penland/Sandbox_1/1/1'>TextToBeDisplayed</scene><br /> <br /> <scene name='Carrie_Morrison_Penland/Sandbox_1/1/6'>TextToBeDisplayed</scene><br /> <br /> <scene name='Carrie_Morrison_Penland/Sandbox_1/1/1'>original</scene><br /> <br /> <scene name='Carrie_Morrison_Penland/Sandbox_1/2efg/1'>TextToBeDisplayed</scene><br /> <br /> <scene name='Carrie_Morrison_Penland/Sandbox_1/2efg/2'>TextToBeDisplayed</scene></div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=Carrie_Morrison_Penland/Sandbox_1&diff=1056163 Carrie Morrison Penland/Sandbox 1 2010-03-16T18:12:22Z

<p>Carrie Morrison Penland: </p> <hr /> <div><applet size='[450,338]' frame='true' align='right'<br /> caption='YYY' /><br /> <scene name='Carrie_Morrison_Penland/Sandbox_1/1/1'>TextToBeDisplayed</scene><br /> <br /> <scene name='Carrie_Morrison_Penland/Sandbox_1/1/1'>TextToBeDisplayed</scene><br /> <br /> <scene name='Carrie_Morrison_Penland/Sandbox_1/1/6'>TextToBeDisplayed</scene><br /> <br /> <scene name='Carrie_Morrison_Penland/Sandbox_1/1/1'>original</scene><br /> <br /> <scene name='Carrie_Morrison_Penland/Sandbox_1/2efg/1'>TextToBeDisplayed</scene><br /> <br /> <scene name='Carrie_Morrison_Penland/Sandbox_1/2efg/2'>TextToBeDisplayed</scene></div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=Carrie_Morrison_Penland/Sandbox_1&diff=1056162 Carrie Morrison Penland/Sandbox 1 2010-03-16T17:58:09Z

<p>Carrie Morrison Penland: </p> <hr /> <div><applet size='[450,338]' frame='true' align='right'<br /> caption='YYY' /><br /> <scene name='Carrie_Morrison_Penland/Sandbox_1/1/1'>TextToBeDisplayed</scene><br /> <br /> <scene name='Carrie_Morrison_Penland/Sandbox_1/1/1'>TextToBeDisplayed</scene><br /> <br /> <scene name='Carrie_Morrison_Penland/Sandbox_1/1/6'>TextToBeDisplayed</scene><br /> <br /> <scene name='Carrie_Morrison_Penland/Sandbox_1/1/1'>original</scene></div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=Carrie_Morrison_Penland/Sandbox_1&diff=1056161 Carrie Morrison Penland/Sandbox 1 2010-03-16T17:55:21Z

<p>Carrie Morrison Penland: </p> <hr /> <div><applet size='[450,338]' frame='true' align='right'<br /> caption='YYY' /><br /> <scene name='Carrie_Morrison_Penland/Sandbox_1/1/1'>TextToBeDisplayed</scene><br /> <br /> <scene name='Carrie_Morrison_Penland/Sandbox_1/1/1'>TextToBeDisplayed</scene><br /> <br /> <scene name='Carrie_Morrison_Penland/Sandbox_1/1/6'>TextToBeDisplayed</scene></div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=Carrie_Morrison_Penland/Sandbox_1&diff=1056156 Carrie Morrison Penland/Sandbox 1 2010-03-16T17:12:57Z

<p>Carrie Morrison Penland: </p> <hr /> <div><br /> <applet size='[450,338]' frame='true' align='right'<br /> caption='YYY' /></div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=Carrie_Morrison_Penland/Sandbox_1&diff=1056155 Carrie Morrison Penland/Sandbox 1 2010-03-16T17:10:28Z

<p>Carrie Morrison Penland: </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_3cin | PDB=3cin | SCENE= }}<br /> xxx</div>

Carrie Morrison Penland https://proteopedia.org/index.php?title=Carrie_Morrison_Penland/Sandbox_1&diff=1056154 Carrie Morrison Penland/Sandbox 1 2010-03-16T17:10:07Z

<p>Carrie Morrison Penland: 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_3cin | PDB=3cin | SCENE= }}</div>

Carrie Morrison Penland