Proteopedia - User contributions [en]

User:Yuan-Ping Pang/HAB•BoNTAe

2010-03-11T16:14:10Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>[http://ovidsp.tx.ovid.com/sp-2.3/ovidweb.cgi?&S=DOIGFPNAOODDJGOPNCELBHJLBPBGAA00&Link+Set=S.sh.15.16.19.40%7c11%7csl_10 Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 1998]</ref><ref>[http://ovidsp.tx.ovid.com/sp-2.3/ovidweb.cgi?&S=IMDCFPMAJEDDJGMPNCELMGJLLMPLAA00&Link+Set=S.sh.15.16.19.40%7c35%7csl_10 Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 2001]</ref><ref>[http://www3.interscience.wiley.com/journal/122456643/abstract U.S. Army Botulinum Neurotoxin (BoNT) medical therapeutics research program: Past accomplishments and future directions, Drug Dev Res 70:266-278 2009]</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 2006]</ref><ref>[http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 2007]</ref><ref>[http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 2009]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods used for generating HAB•BoNTAe, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

Download the coordinates of Models [http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb 1 (Hab1.pdb)], [http://www.proteopedia.org/wiki/images/f/f7/Hab2.pdb 2 (Hab2.pdb)], and [http://www.proteopedia.org/wiki/images/5/59/Hab3.pdb 3 (Hab3.pdb)] (PDB format)

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-11T04:28:34Z

Yuan-Ping Pang: Replacing page with 'This is a test.'

This is a test.

User:Yuan-Ping Pang/HAB•BoNTAe

2010-03-11T04:21:54Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>[http://ovidsp.tx.ovid.com/sp-2.3/ovidweb.cgi?&S=DOIGFPNAOODDJGOPNCELBHJLBPBGAA00&Link+Set=S.sh.15.16.19.40%7c11%7csl_10 Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 1998]</ref><ref>[http://ovidsp.tx.ovid.com/sp-2.3/ovidweb.cgi?&S=IMDCFPMAJEDDJGMPNCELMGJLLMPLAA00&Link+Set=S.sh.15.16.19.40%7c35%7csl_10 Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 2001]</ref><ref>[http://www3.interscience.wiley.com/journal/122456643/abstract U.S. Army Botulinum Neurotoxin (BoNT) medical therapeutics research program: Past accomplishments and future directions Drug Dev Res 70:266-278 2009]</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 2006]</ref><ref>[http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 2007]</ref><ref>[http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 2009]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the accuracy of the computational methods used for generating HAB•BoNTAe, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

Download the coordinates of Models [http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb 1 (Hab1.pdb)], [http://www.proteopedia.org/wiki/images/f/f7/Hab2.pdb 2 (Hab2.pdb)], and [http://www.proteopedia.org/wiki/images/5/59/Hab3.pdb 3 (Hab3.pdb)] (PDB format)

References & Notes
<references/>

Proteopedia:Table of Contents

2010-03-11T04:19:31Z

Yuan-Ping Pang:

This guide to the contents of Proteopedia is maintained manually (not automatically generated) and so is inevitably incomplete. Please be sure to use the [[Help:Searching|search slots at the left]] if you don't find what you are looking for below.

<big>
{{#tree:id=siteTree|openlevels=1|close=top|open=top|

* Introduction to Structural Biology
** See [[About Macromolecular Structure]]
** Water

*** [[Water in macromolecular models|Water in Macromolecular Models]]
** Key Chemical Concepts for Structural Biology

*** [[Amino Acids]]
*** [[Cation-pi interactions]]
*** [[Hydrogen bond]]
*** [[Hydrogen in macromolecular models|Hydrogen in Macromolecular Models]]
*** [[Isoelectric point]]
*** [[Salt bridges]]

* Biomolecules
** [[About Macromolecular Structure]]

** Nucleotides, Nucleic Acids and Genetic Information
*** DNA
**** [[DNA]]
**** B-DNA [[1bna]]
**** [[Z-DNA]]

** Amino Acids
*** [[Amino Acids]]
*** [[Selenocysteine]]
** Proteins, Primary Structure
*** [[Conservation, Evolutionary]]
*** [[Isoelectric point]]

** Proteins, Three-Dimensional Structure
*** [[User:Tommie_Hata/Protein_Structure_Tutorial]]
*** [[S347/The four tiers of protein structure]]
*** [[Secondary structure]]
*** Protein structural motifs
**** [[User:James D Watson/Structural Templates]]
*** Fibrous Proteins
**** [[Coiled coil]]
**** [[Collagen]]
*** Protein Misfolding
**** [[Prion protein]]
**** [[A Physical Model of the Structure of GNNQQNY from Yeast Prion Sup35]]

** Colored Proteins & those that Change Color
*** [[Green Fluorescent Protein]]; [[GFP (Hebrew)]]
*** [[Dronpa]]
*** [[Factor IX]]

** DNA Binding Proteins
*** [[Helix-turn-helix motif]]
*** [[DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1]]

** Protein Function: Myoglobin and Hemoglobin, Muscle Contraction, and Antibodies
*** Antibodies
**** [[IgA]]
**** [[Epitopes]]
**** [[Major Histocompatibility Complex Class I]]
*** [[Calmodulin in motion]]
*** [[Myoglobin]]
*** [[Hemoglobin]]; [[Hemoglobin (Hebrew)]]
*** [[Kinesin-5]]
** Lipids and Biological Membranes
** Lipid Binding Proteins
*** [[CRABP I ( Cellular Retinoic Acid Binding Protein )]]
** Membrane Transport Proteins
*** [[A Physical Model of the β2-Adrenergic Receptor]]
*** [[Lactose Permease]]
*** [[Proton Channels]]
*** [[Ion channels]]
**** [[M2 Proton Channel]]
**** [[Voltage-gated calcium channels]]
*** [[Mechanosensitive channels: opening and closing]]
***[[Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System]]

** Prions and Intrinsically Disordered Proteins
*** [[Prion protein]]
*** [[Doppel]]
*** [[Intrinsically Disordered Protein]]

** Toxins
*** [[Insecticidal delta-endotoxin Cyt2Ba from Bacillus thuringiensis]]

** Mitosis, Meiosis and Cargo Transport Proteins
*** [[Kinesin-5]]

** Viruses
*** [[User:Wayne Decatur/Suppression of RNA Silencing by Viruses]]
*** Filamentous bacteriphage
**** [[G3p]] - minor coat protein found on the surface of filamentous bacteriophage
*** HIV
**** [[HIV-1 protease]]
**** [[HIV-1 Gag]]
**** [[HIV-1 Gag Recruitment of Tsg101 and the Viral Budding Process]]
**** [[User:Eric Martz/Molecular Playground/HIVDrug]]
*** Herpes Simplex Virus
**** [[Herpes Simplex Virus Thymidine Kinase]]
*** Influenza
**** [[Influenza hemagglutinin]]
**** [[Avian Influenza Neuraminidase, Tamiflu and Relenza]]

* Enzymes
** Enzymatic Catalysis
*** Acid-beta-glucosidase
**** reHuman Acid-beta-glucosidase made in CHO cells [[1ogs]]
**** reHuman Acid-beta-glucosidase made in CHO cells bound to conduritol B epoxide [[1y7v]]
**** reHuman Acid-beta-glucosidase made in carrot cells complexed with N-butyl-deoxynojirimycin [[2v3d]]
**** Velaglucerase Alfa [[2wkl]]
*** Acid Proteases
**** [[HIV-1 protease]]

**** [[Streptomyces griseus Aminopeptidase (SGAP)]]; [[Aminopeptidase]]
*** [[Aconitase]]
*** Cysteine Proteases
*** [[Hen Egg-White (HEW) Lysozyme]]
*** [[Choline Oxidase]]
*** [[Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System]]
*** [[Metalloproteases]]
**** [[Matrix metalloproteinases]]
*** Oxidoreductases
**** [[NADH quinone oxidoreductase ]]
*** [[Phosphofructokinase %28PFK%29]]
*** [[Pyruvate phosphate dikinase]]
*** [[Serotonin N-acetyltransferase]]
*** Serine Hydrolases
**** [[Acetylcholinesterase]] (AChE)
***** [[Acetylcholine]]
***** [[Flexibility of aromatic residues in acetylcholinesterase]]
***** [[AChE inhibitors and substrates]]
****** [[1eve]] AChE-Aricept complex; [[1eve (Arabic)]]; [[1eve (Chinese)]]; [[1eve (Italian)]]; [[1eve (Russian)]]; [[1eve (Spanish)]]; [[1eve (Turkish)]]
****** [[AChE bivalent inhibitors]]
**** [[Tobacco Etch Virus (TEV) Protease]]
*** [[Serine Protease]]
**** [[Trypsin]]
*** [[Triose Phosphate Isomerase]]
** Enzyme Inhibitors
*** [[Alpha-1-antitrypsin]]
** Enzyme Kinetics, Inhibition, and Control
***[[Avian Influenza Neuraminidase, Tamiflu and Relenza]]
** Biochemical Signaling
*** [[Nitric oxide synthase]], [[NOS structures]]
*** [[Recoverin, a calcium-activated myristoyl switch]]
*** [[Bcl-2]]
*** [[C-Myc]]
*** [[C-di-GMP signaling]]

** Enzymes - Molecular Machines
*** [[Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System]]
*** [[Pyruvate phosphate dikinase]]

* Metabolism
** Introduction to Metabolism

** Glucose Catabolism
*** [[Triose Phosphate Isomerase]]
***[[Phosphofructokinase %28PFK%29]]

** Glycogen Metabolism and Gluconeogenesis
*** [[Phosphoglucose isomerase]]
*** [[Calmodulin in motion]]
*** [[Biotin Protein Ligase]]

** Citric Acid Cycle
*** [[Aconitase]]

** Electron Transport and Oxidative Phosphorylation
*** [[NADH quinone oxidoreductase ]]

** Photosynthesis
*** [[Photosystem II]]
*** [[Ribulose-1,5-bisphosphate carboxylase/oxygenase]]
*** [[PrrA in Rhodobacter sphaeroides]]
*** [[Pyruvate phosphate dikinase]]

** Lipid Metabolism
*** [[Acid-beta-glucosidase]]
** Amino Acid Metabolism
*** [[Aromatic amino acid hydroxylases]]
*** [[Phenylalanine hydroxylase]]
*** [[Tyrosine hydroxylase]]
*** [[ATP Phosphoribosyl Transferase]]
*** [[Isochorismate pyruvate lyase]]
** Mammalian Fuel Metabolism: Integration and Regulation
** Nucleotide Metabolism
*** [[Dihydrofolate reductase]]

* Gene Expression and Replication

** Nucleic Acid Structure
*** [[DNA]]
**** B-DNA [[1bna]]
**** [[Z-DNA]]
*** [[Nucleosomes]]

** DNA Replication, Repair, and Recombination
*** [[DNA Replication,Transcription and Translation]]
*** [[DNA Polymerase I]]
*** [[PcrA helicase]]
*** [[Fpg Nei Protein Superfamily]] - DNA Repair and Base Excision DNA Repair
*** [[Human RecQ-Like protein 1]] - RecQ family of DNA helicases are conserved in from bacteria to man
*** [[Structure of E. coli DnaC helicase loader]]
***[[1x9n#Crystal Structure of Human DNA Ligase I bound to 5.27-adenylated.2C nicked DNA]]
*** [[Rop protein]]

** Transcription and RNA Processing
*** [[C-Myc]]
*** [[Lac repressor]]
*** [[Reverse transcriptase]]
*** [[TATA-Binding Protein]]
*** [[RSP1275]]
*** [[Transcription Termination Factor Rho]]

** Protein Synthesis
*** [[Ribosome]]
*** [[SelB Recognition]]
** Regulation of Gene Expression
*** [[Lac repressor]]
*** [[Irr]] (Iron Response Regulator )
*** Oncogenes
**** [[P53]]
**** [[SRC]]
*** [[Tangible Models of Cdc42 Interacting With Intersectin]]

* Evolution
** [[Conservation, Evolutionary]]

** [[Extremophiles]]

* Immune System
** Antibodies
*** [[IgA]]
*** [[Epitopes]]
** [[Major Histocompatibility Complex Class I]]
*** [[Human beta two microglobulin]]

* Diseases
** Cancer
*** [[SRC]]
*** [[Proteins involved in cancer]]

* Methods of Structure Determination
** X-ray
*** [[X-ray crystallography]]
**** [[Asymmetric Unit]]
**** [[Biological Unit]]
**** [[Electron density maps]]
*** SAXS
** NMR
*** [[NMR Ensembles of Models]]
** Electron Microscopy

* Methods of Structure & Sequence Analysis
** Structural Analysis & Visualization
*** [[CPK]] - Corey-Pauling-Koltun spacefilling molecular models and color scheme for elements
*** [[Chime]]
*** Jmol
**** [[S347/Visualising protein structure|Visualising Protein Structure]] - Introduction to Jmol
**** [[FirstGlance in Jmol]]
*** [[User:Wayne Decatur/Teaching Proteopedia|Teaching Proteopedia]]
*** [[User:Wayne Decatur/Generate Unfolded Structures|Generate Unfolded Structures]]
*** Homology Model
**** [[User:Wayne Decatur/Homology Modeling|Homology Modeling]]
**** [[User:Emi Nakayama/TRIM5a Homology Models|TRIM5a Homology Models]] - Differences in models as a function of their templates
*** [[DRuMS]] - set of standard color schemes for macromolecular visualization

** Sequence Analysis
*** [[User:Wayne Decatur/Sequence analysis tools|Sequence Analysis Tools]]

* Model Structures
** See [[Theoretical models]]
** [[African Malaria Mosquito Acetylcholinesterase]]
** [[Structure of E. coli DnaC helicase loader]]
** [[User:Yuan-Ping Pang/HAB•BoNTAe]]

* Miscellaneous
** [[Molecular Playground]]
** [[Research Groups]]
}}
</big>

Proteopedia:Table of Contents

2010-03-11T04:15:27Z

Yuan-Ping Pang:

This guide to the contents of Proteopedia is maintained manually (not automatically generated) and so is inevitably incomplete. Please be sure to use the [[Help:Searching|search slots at the left]] if you don't find what you are looking for below.

<big>
{{#tree:id=siteTree|openlevels=1|close=top|open=top|

* Introduction to Structural Biology
** See [[About Macromolecular Structure]]
** Water

*** [[Water in macromolecular models|Water in Macromolecular Models]]
** Key Chemical Concepts for Structural Biology

*** [[Amino Acids]]
*** [[Cation-pi interactions]]
*** [[Hydrogen bond]]
*** [[Hydrogen in macromolecular models|Hydrogen in Macromolecular Models]]
*** [[Isoelectric point]]
*** [[Salt bridges]]

* Biomolecules
** [[About Macromolecular Structure]]

** Nucleotides, Nucleic Acids and Genetic Information
*** DNA
**** [[DNA]]
**** B-DNA [[1bna]]
**** [[Z-DNA]]

** Amino Acids
*** [[Amino Acids]]
*** [[Selenocysteine]]
** Proteins, Primary Structure
*** [[Conservation, Evolutionary]]
*** [[Isoelectric point]]

** Proteins, Three-Dimensional Structure
*** [[User:Tommie_Hata/Protein_Structure_Tutorial]]
*** [[S347/The four tiers of protein structure]]
*** [[Secondary structure]]
*** Protein structural motifs
**** [[User:James D Watson/Structural Templates]]
*** Fibrous Proteins
**** [[Coiled coil]]
**** [[Collagen]]
*** Protein Misfolding
**** [[Prion protein]]
**** [[A Physical Model of the Structure of GNNQQNY from Yeast Prion Sup35]]

** Colored Proteins & those that Change Color
*** [[Green Fluorescent Protein]]; [[GFP (Hebrew)]]
*** [[Dronpa]]
*** [[Factor IX]]

** DNA Binding Proteins
*** [[Helix-turn-helix motif]]
*** [[DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1]]

** Protein Function: Myoglobin and Hemoglobin, Muscle Contraction, and Antibodies
*** Antibodies
**** [[IgA]]
**** [[Epitopes]]
**** [[Major Histocompatibility Complex Class I]]
*** [[Calmodulin in motion]]
*** [[Myoglobin]]
*** [[Hemoglobin]]; [[Hemoglobin (Hebrew)]]
*** [[Kinesin-5]]
** Lipids and Biological Membranes
** Lipid Binding Proteins
*** [[CRABP I ( Cellular Retinoic Acid Binding Protein )]]
** Membrane Transport Proteins
*** [[A Physical Model of the β2-Adrenergic Receptor]]
*** [[Lactose Permease]]
*** [[Proton Channels]]
*** [[Ion channels]]
**** [[M2 Proton Channel]]
**** [[Voltage-gated calcium channels]]
*** [[Mechanosensitive channels: opening and closing]]
***[[Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System]]

** Prions and Intrinsically Disordered Proteins
*** [[Prion protein]]
*** [[Doppel]]
*** [[Intrinsically Disordered Protein]]

** Toxins
*** [[Insecticidal delta-endotoxin Cyt2Ba from Bacillus thuringiensis]]

** Mitosis, Meiosis and Cargo Transport Proteins
*** [[Kinesin-5]]

** Viruses
*** [[User:Wayne Decatur/Suppression of RNA Silencing by Viruses]]
*** Filamentous bacteriphage
**** [[G3p]] - minor coat protein found on the surface of filamentous bacteriophage
*** HIV
**** [[HIV-1 protease]]
**** [[HIV-1 Gag]]
**** [[HIV-1 Gag Recruitment of Tsg101 and the Viral Budding Process]]
**** [[User:Eric Martz/Molecular Playground/HIVDrug]]
*** Herpes Simplex Virus
**** [[Herpes Simplex Virus Thymidine Kinase]]
*** Influenza
**** [[Influenza hemagglutinin]]
**** [[Avian Influenza Neuraminidase, Tamiflu and Relenza]]

* Enzymes
** Enzymatic Catalysis
*** Acid-beta-glucosidase
**** reHuman Acid-beta-glucosidase made in CHO cells [[1ogs]]
**** reHuman Acid-beta-glucosidase made in CHO cells bound to conduritol B epoxide [[1y7v]]
**** reHuman Acid-beta-glucosidase made in carrot cells complexed with N-butyl-deoxynojirimycin [[2v3d]]
**** Velaglucerase Alfa [[2wkl]]
*** Acid Proteases
**** [[HIV-1 protease]]

**** [[Streptomyces griseus Aminopeptidase (SGAP)]]; [[Aminopeptidase]]
*** [[Aconitase]]
*** Cysteine Proteases
*** [[Hen Egg-White (HEW) Lysozyme]]
*** [[Choline Oxidase]]
*** [[Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System]]
*** [[Metalloproteases]]
**** [[Matrix metalloproteinases]]
*** Oxidoreductases
**** [[NADH quinone oxidoreductase ]]
*** [[Phosphofructokinase %28PFK%29]]
*** [[Pyruvate phosphate dikinase]]
*** [[Serotonin N-acetyltransferase]]
*** Serine Hydrolases
**** [[Acetylcholinesterase]] (AChE)
***** [[Acetylcholine]]
***** [[Flexibility of aromatic residues in acetylcholinesterase]]
***** [[AChE inhibitors and substrates]]
****** [[1eve]] AChE-Aricept complex; [[1eve (Arabic)]]; [[1eve (Chinese)]]; [[1eve (Italian)]]; [[1eve (Russian)]]; [[1eve (Spanish)]]; [[1eve (Turkish)]]
****** [[AChE bivalent inhibitors]]
**** [[Tobacco Etch Virus (TEV) Protease]]
*** [[Serine Protease]]
**** [[Trypsin]]
*** [[Triose Phosphate Isomerase]]
** Enzyme Inhibitors
*** [[Alpha-1-antitrypsin]]
** Enzyme Kinetics, Inhibition, and Control
***[[Avian Influenza Neuraminidase, Tamiflu and Relenza]]
** Biochemical Signaling
*** [[Nitric oxide synthase]], [[NOS structures]]
*** [[Recoverin, a calcium-activated myristoyl switch]]
*** [[Bcl-2]]
*** [[C-Myc]]
*** [[C-di-GMP signaling]]

** Enzymes - Molecular Machines
*** [[Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System]]
*** [[Pyruvate phosphate dikinase]]

* Metabolism
** Introduction to Metabolism

** Glucose Catabolism
*** [[Triose Phosphate Isomerase]]
***[[Phosphofructokinase %28PFK%29]]

** Glycogen Metabolism and Gluconeogenesis
*** [[Phosphoglucose isomerase]]
*** [[Calmodulin in motion]]
*** [[Biotin Protein Ligase]]

** Citric Acid Cycle
*** [[Aconitase]]

** Electron Transport and Oxidative Phosphorylation
*** [[NADH quinone oxidoreductase ]]

** Photosynthesis
*** [[Photosystem II]]
*** [[Ribulose-1,5-bisphosphate carboxylase/oxygenase]]
*** [[PrrA in Rhodobacter sphaeroides]]
*** [[Pyruvate phosphate dikinase]]

** Lipid Metabolism
*** [[Acid-beta-glucosidase]]
** Amino Acid Metabolism
*** [[Aromatic amino acid hydroxylases]]
*** [[Phenylalanine hydroxylase]]
*** [[Tyrosine hydroxylase]]
*** [[ATP Phosphoribosyl Transferase]]
*** [[Isochorismate pyruvate lyase]]
** Mammalian Fuel Metabolism: Integration and Regulation
** Nucleotide Metabolism
*** [[Dihydrofolate reductase]]

* Gene Expression and Replication

** Nucleic Acid Structure
*** [[DNA]]
**** B-DNA [[1bna]]
**** [[Z-DNA]]
*** [[Nucleosomes]]

** DNA Replication, Repair, and Recombination
*** [[DNA Replication,Transcription and Translation]]
*** [[DNA Polymerase I]]
*** [[PcrA helicase]]
*** [[Fpg Nei Protein Superfamily]] - DNA Repair and Base Excision DNA Repair
*** [[Human RecQ-Like protein 1]] - RecQ family of DNA helicases are conserved in from bacteria to man
*** [[Structure of E. coli DnaC helicase loader]]
***[[1x9n#Crystal Structure of Human DNA Ligase I bound to 5.27-adenylated.2C nicked DNA]]
*** [[Rop protein]]

** Transcription and RNA Processing
*** [[C-Myc]]
*** [[Lac repressor]]
*** [[Reverse transcriptase]]
*** [[TATA-Binding Protein]]
*** [[RSP1275]]
*** [[Transcription Termination Factor Rho]]

** Protein Synthesis
*** [[Ribosome]]
*** [[SelB Recognition]]
** Regulation of Gene Expression
*** [[Lac repressor]]
*** [[Irr]] (Iron Response Regulator )
*** Oncogenes
**** [[P53]]
**** [[SRC]]
*** [[Tangible Models of Cdc42 Interacting With Intersectin]]

* Evolution
** [[Conservation, Evolutionary]]

** [[Extremophiles]]

* Immune System
** Antibodies
*** [[IgA]]
*** [[Epitopes]]
** [[Major Histocompatibility Complex Class I]]
*** [[Human beta two microglobulin]]

* Diseases
** Cancer
*** [[SRC]]
*** [[Proteins involved in cancer]]

* Methods of Structure Determination
** X-ray
*** [[X-ray crystallography]]
**** [[Asymmetric Unit]]
**** [[Biological Unit]]
**** [[Electron density maps]]
*** SAXS
** NMR
*** [[NMR Ensembles of Models]]
** Electron Microscopy

* Methods of Structure & Sequence Analysis
** Structural Analysis & Visualization
*** [[CPK]] - Corey-Pauling-Koltun spacefilling molecular models and color scheme for elements
*** [[Chime]]
*** Jmol
**** [[S347/Visualising protein structure|Visualising Protein Structure]] - Introduction to Jmol
**** [[FirstGlance in Jmol]]
*** [[User:Wayne Decatur/Teaching Proteopedia|Teaching Proteopedia]]
*** [[User:Wayne Decatur/Generate Unfolded Structures|Generate Unfolded Structures]]
*** Homology Model
**** [[User:Wayne Decatur/Homology Modeling|Homology Modeling]]
**** [[User:Emi Nakayama/TRIM5a Homology Models|TRIM5a Homology Models]] - Differences in models as a function of their templates
*** [[DRuMS]] - set of standard color schemes for macromolecular visualization

** Sequence Analysis
*** [[User:Wayne Decatur/Sequence analysis tools|Sequence Analysis Tools]]

* Model Structures
** See [[Theoretical models]]
** [[African Malaria Mosquito Acetylcholinesterase]]
** [[Structure of E. coli DnaC helicase loader]]
** [[Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB]]

* Miscellaneous
** [[Molecular Playground]]
** [[Research Groups]]
}}
</big>

User:Yuan-Ping Pang/HAB•BoNTAe

2010-03-11T04:10:22Z

Yuan-Ping Pang: New page: This is a test.

This is a test.

User:Yuan-Ping Pang/Sandbox 1

2010-03-11T03:54:38Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>[http://ovidsp.tx.ovid.com/sp-2.3/ovidweb.cgi?&S=DOIGFPNAOODDJGOPNCELBHJLBPBGAA00&Link+Set=S.sh.15.16.19.40%7c11%7csl_10 Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 1998]</ref><ref>[http://ovidsp.tx.ovid.com/sp-2.3/ovidweb.cgi?&S=IMDCFPMAJEDDJGMPNCELMGJLLMPLAA00&Link+Set=S.sh.15.16.19.40%7c35%7csl_10 Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 2001]</ref><ref>[http://www3.interscience.wiley.com/journal/122456643/abstract U.S. Army Botulinum Neurotoxin (BoNT) medical therapeutics research program: Past accomplishments and future directions Drug Dev Res 70:266-278 2009]</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 2006]</ref><ref>[http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 2007]</ref><ref>[http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 2009]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the accuracy of the computational methods used for generating HAB•BoNTAe, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

Download the coordinates of Models [http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb 1 (Hab1.pdb)], [http://www.proteopedia.org/wiki/images/f/f7/Hab2.pdb 2 (Hab2.pdb)], and [http://www.proteopedia.org/wiki/images/5/59/Hab3.pdb 3 (Hab3.pdb)] (PDB format)

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-11T03:53:01Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>[http://ovidsp.tx.ovid.com/sp-2.3/ovidweb.cgi?&S=DOIGFPNAOODDJGOPNCELBHJLBPBGAA00&Link+Set=S.sh.15.16.19.40%7c11%7csl_10 Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 1998]</ref><ref>[http://ovidsp.tx.ovid.com/sp-2.3/ovidweb.cgi?&S=IMDCFPMAJEDDJGMPNCELMGJLLMPLAA00&Link+Set=S.sh.15.16.19.40%7c35%7csl_10 Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 2001]</ref><ref>[http://www3.interscience.wiley.com/journal/122456643/abstract U.S. Army Botulinum Neurotoxin (BoNT) medical therapeutics research program: Past accomplishments and future directions Drug Dev Res 70:266-278 2009]</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 2006]</ref><ref>[http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 2007]</ref><ref>[http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 2009]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the accuracy of the computational methods for generating HAB•BoNTAe, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

Download the coordinates of Models [http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb 1 (Hab1.pdb)], [http://www.proteopedia.org/wiki/images/f/f7/Hab2.pdb 2 (Hab2.pdb)], and [http://www.proteopedia.org/wiki/images/5/59/Hab3.pdb 3 (Hab3.pdb)] (PDB format)

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-11T03:46:18Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>[http://ovidsp.tx.ovid.com/sp-2.3/ovidweb.cgi?&S=DOIGFPNAOODDJGOPNCELBHJLBPBGAA00&Link+Set=S.sh.15.16.19.40%7c11%7csl_10 Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 1998]</ref><ref>[http://ovidsp.tx.ovid.com/sp-2.3/ovidweb.cgi?&S=IMDCFPMAJEDDJGMPNCELMGJLLMPLAA00&Link+Set=S.sh.15.16.19.40%7c35%7csl_10 Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 2001]</ref><ref>[http://www3.interscience.wiley.com/journal/122456643/abstract U.S. Army Botulinum Neurotoxin (BoNT) medical therapeutics research program: Past accomplishments and future directions Drug Dev Res 70:266-278 2009]</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 2006]</ref><ref>[http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 2007]</ref><ref>[http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 2009]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

Download the coordinates of Models [http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb 1 (Hab1.pdb)], [http://www.proteopedia.org/wiki/images/f/f7/Hab2.pdb 2 (Hab2.pdb)], and [http://www.proteopedia.org/wiki/images/5/59/Hab3.pdb 3 (Hab3.pdb)] (PDB format)

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-11T03:45:14Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>[http://ovidsp.tx.ovid.com/sp-2.3/ovidweb.cgi?&S=DOIGFPNAOODDJGOPNCELBHJLBPBGAA00&Link+Set=S.sh.15.16.19.40%7c11%7csl_10 Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)]</ref><ref>[http://ovidsp.tx.ovid.com/sp-2.3/ovidweb.cgi?&S=IMDCFPMAJEDDJGMPNCELMGJLLMPLAA00&Link+Set=S.sh.15.16.19.40%7c35%7csl_10 Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)]</ref><ref>[http://www3.interscience.wiley.com/journal/122456643/abstract U.S. Army Botulinum Neurotoxin (BoNT) medical therapeutics research program: Past accomplishments and future directions Drug Dev Res 70:266-278 2009]</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 2006]</ref><ref>[http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 2007]</ref><ref>[http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 2009]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

Download the coordinates of Models [http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb 1 (Hab1.pdb)], [http://www.proteopedia.org/wiki/images/f/f7/Hab2.pdb 2 (Hab2.pdb)], and [http://www.proteopedia.org/wiki/images/5/59/Hab3.pdb 3 (Hab3.pdb)] (PDB format)

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-10T01:28:38Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>[http://ovidsp.tx.ovid.com/sp-2.3/ovidweb.cgi?&S=DOIGFPNAOODDJGOPNCELBHJLBPBGAA00&Link+Set=S.sh.15.16.19.40%7c11%7csl_10 Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)]</ref><ref>[http://ovidsp.tx.ovid.com/sp-2.3/ovidweb.cgi?&S=IMDCFPMAJEDDJGMPNCELMGJLLMPLAA00&Link+Set=S.sh.15.16.19.40%7c35%7csl_10 Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)]</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 (2006)]</ref><ref>[http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 (2007)]</ref><ref>[http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 (2009)]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

Download the coordinates of Models [http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb 1 (Hab1.pdb)], [http://www.proteopedia.org/wiki/images/f/f7/Hab2.pdb 2 (Hab2.pdb)], and [http://www.proteopedia.org/wiki/images/5/59/Hab3.pdb 3 (Hab3.pdb)] (PDB format)

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-10T01:27:12Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>[http://ovidsp.tx.ovid.com/sp-2.3/ovidweb.cgi?&S=DOIGFPNAOODDJGOPNCELBHJLBPBGAA00&Link+Set=S.sh.15.16.19.40%7c11%7csl_10 Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)]</ref><ref>[http://ovidsp.tx.ovid.com/sp-2.3/ovidweb.cgi?&S=IMDCFPMAJEDDJGMPNCELMGJLLMPLAA00&Link+Set=S.sh.15.16.19.40%7c35%7csl_10 Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)]</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 (2006)]</ref><ref>[http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 (2007)]</ref><ref>[http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 (2009)]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

Download the coordinates of [http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb Model 1 (Hab1.pdb)], [http://www.proteopedia.org/wiki/images/f/f7/Hab2.pdb Model 2 (Hab2.pdb)], and [http://www.proteopedia.org/wiki/images/5/59/Hab3.pdb Model 3 (Hab3.pdb)] (PDB format)

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-10T01:25:49Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>[http://ovidsp.tx.ovid.com/sp-2.3/ovidweb.cgi?&S=DOIGFPNAOODDJGOPNCELBHJLBPBGAA00&Link+Set=S.sh.15.16.19.40%7c11%7csl_10 Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)]</ref><ref>[http://ovidsp.tx.ovid.com/sp-2.3/ovidweb.cgi?&S=IMDCFPMAJEDDJGMPNCELMGJLLMPLAA00&Link+Set=S.sh.15.16.19.40%7c35%7csl_10 Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)]</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 (2006)]</ref><ref>[http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 (2007)]</ref><ref>[http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 (2009)]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

Download the coordinates of [http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb Model 1 (Hab1.pdb)] [http://www.proteopedia.org/wiki/images/f/f7/Hab2.pdb Model 2 (Hab2.pdb)] [http://www.proteopedia.org/wiki/images/5/59/Hab3.pdb Model 3 (Hab3.pdb)] (PDB format)

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-10T01:21:43Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>[http://ovidsp.tx.ovid.com/sp-2.3/ovidweb.cgi?&S=DOIGFPNAOODDJGOPNCELBHJLBPBGAA00&Link+Set=S.sh.15.16.19.40%7c11%7csl_10 Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)]</ref><ref>[http://ovidsp.tx.ovid.com/sp-2.3/ovidweb.cgi?&S=IMDCFPMAJEDDJGMPNCELMGJLLMPLAA00&Link+Set=S.sh.15.16.19.40%7c35%7csl_10 Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)]</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 (2006)]</ref><ref>[http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 (2007)]</ref><ref>[http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 (2009)]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb Download the coordinates of Model 1 (Hab1.pdb, PDB format)]

[http://www.proteopedia.org/wiki/images/f/f7/Hab2.pdb Download the coordinates of Model 2 (Hab2.pdb, PDB format)]

[http://www.proteopedia.org/wiki/images/5/59/Hab3.pdb Download the coordinates of Model 3 (Hab3.pdb, PDB format)]

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-10T01:19:04Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>[http://ovidsp.tx.ovid.com/sp-2.3/ovidweb.cgi?&S=DOIGFPNAOODDJGOPNCELBHJLBPBGAA00&Link+Set=S.sh.15.16.19.40%7c11%7csl_10 Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)]</ref><ref>Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 (2006)]</ref><ref>[http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 (2007)]</ref><ref>[http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 (2009)]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb Download the coordinates of Model 1 (Hab1.pdb, PDB format)]

[http://www.proteopedia.org/wiki/images/f/f7/Hab2.pdb Download the coordinates of Model 2 (Hab2.pdb, PDB format)]

[http://www.proteopedia.org/wiki/images/5/59/Hab3.pdb Download the coordinates of Model 3 (Hab3.pdb, PDB format)]

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-10T01:10:56Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)</ref><ref>Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 (2006)]</ref><ref>[http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 (2007)]</ref><ref>[http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 (2009)]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb Download the coordinates of Model 1 (Hab1.pdb, PDB format)]

[http://www.proteopedia.org/wiki/images/f/f7/Hab2.pdb Download the coordinates of Model 2 (Hab2.pdb, PDB format)]

[http://www.proteopedia.org/wiki/images/5/59/Hab3.pdb Download the coordinates of Model 3 (Hab3.pdb, PDB format)]

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-10T01:08:40Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)</ref><ref>Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 (2006) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 reprint]</ref><ref>[http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 (2007)]</ref><ref>Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 (2009) [http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb Download the coordinates of Model 1 (Hab1.pdb, PDB format)]

[http://www.proteopedia.org/wiki/images/f/f7/Hab2.pdb Download the coordinates of Model 2 (Hab2.pdb, PDB format)]

[http://www.proteopedia.org/wiki/images/5/59/Hab3.pdb Download the coordinates of Model 3 (Hab3.pdb, PDB format)]

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-10T00:53:23Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)</ref><ref>Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 (2006) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 reprint]</ref><ref>Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 (2007) [http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 reprint]</ref><ref>Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 (2009) [http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 reprint]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb Download the coordinates of Model 1 (Hab1.pdb, PDB format)]

[http://www.proteopedia.org/wiki/images/f/f7/Hab2.pdb Download the coordinates of Model 2 (Hab2.pdb, PDB format)]

[http://www.proteopedia.org/wiki/images/5/59/Hab3.pdb Download the coordinates of Model 3 (Hab3.pdb, PDB format)]

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-10T00:52:50Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)</ref><ref>Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 (2006) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 reprint]</ref><ref>Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 (2007) [http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 reprint]</ref><ref>Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 (2009) [http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 reprint]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb Download the coordinates of Model 1 (Hab1.pdb, PDB format)]

[http://www.proteopedia.org/wiki/images/f/f7/Hab2.pdb Download the coordinates of Model 2 (Hab2.pdb, PDB format)]

[http://www.proteopedia.org/wiki/index.php/Image:Hab3.pdb Download the coordinates of Model 3 (Hab3.pdb, PDB format)]

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-10T00:51:38Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)</ref><ref>Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 (2006) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 reprint]</ref><ref>Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 (2007) [http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 reprint]</ref><ref>Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 (2009) [http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 reprint]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb Download the coordinates of Model 1 (Hab1.pdb, PDB format)]

[http://www.proteopedia.org/wiki/index.php/Image:Hab2.pdb Download the coordinates of Model 2 (Hab2.pdb, PDB format)]

[http://www.proteopedia.org/wiki/index.php/Image:Hab3.pdb Download the coordinates of Model 3 (Hab3.pdb, PDB format)]

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-10T00:51:16Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)</ref><ref>Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 (2006) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 reprint]</ref><ref>Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 (2007) [http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 reprint]</ref><ref>Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 (2009) [http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 reprint]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[[http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb Download the coordinates of Model 1 (Hab1.pdb, PDB format)]

[http://www.proteopedia.org/wiki/index.php/Image:Hab2.pdb Download the coordinates of Model 2 (Hab2.pdb, PDB format)]

[http://www.proteopedia.org/wiki/index.php/Image:Hab3.pdb Download the coordinates of Model 3 (Hab3.pdb, PDB format)]

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-09T23:53:35Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)</ref><ref>Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 (2006) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 reprint]</ref><ref>Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 (2007) [http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 reprint]</ref><ref>Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 (2009) [http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 reprint]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[http://www.proteopedia.org/wiki/index.php/Image:Hab1.pdb Download the coordinates of Model 1 (Hab1.pdb, PDB format)]

[http://www.proteopedia.org/wiki/index.php/Image:Hab2.pdb Download the coordinates of Model 2 (Hab2.pdb, PDB format)]

[http://www.proteopedia.org/wiki/index.php/Image:Hab3.pdb Download the coordinates of Model 3 (Hab3.pdb, PDB format)]

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-09T23:44:04Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)</ref><ref>Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 (2006) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 reprint]</ref><ref>Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 (2007) [http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 reprint]</ref><ref>Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 (2009) [http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 reprint]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[http://www.proteopedia.org/wiki/index.php/Image:Hab1.pdb Download the coordinates of Model 1 (PDB format)]

[http://www.proteopedia.org/wiki/index.php/Image:Hab2.pdb Download the coordinates of Model 2 (PDB format)]

[http://www.proteopedia.org/wiki/index.php/Image:Hab3.pdb Download the coordinates of Model 3 (PDB format)]

References & Notes
<references/>

File:Hab3.pdb

2010-03-09T23:42:58Z

Yuan-Ping Pang: Model 3 of HAB•BoNTAe

Model 3 of HAB•BoNTAe

File:Hab2.pdb

2010-03-09T23:42:20Z

Yuan-Ping Pang: Model 2 of HAB•BoNTAe

Model 2 of HAB•BoNTAe

User:Yuan-Ping Pang/Sandbox 1

2010-03-09T23:24:21Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)</ref><ref>Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 (2006) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 reprint]</ref><ref>Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 (2007) [http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 reprint]</ref><ref>Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 (2009) [http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 reprint]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[http://www.proteopedia.org/wiki/index.php/Image:Hab1.pdb Download the coordinates of Model 1 (PDB format)]

[[Download the coordinates of Model 2 (PDB format)]]

[[Download the coordinates of Model 3 (PDB format)]]

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-09T23:23:34Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)</ref><ref>Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 (2006) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 reprint]</ref><ref>Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 (2007) [http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 reprint]</ref><ref>Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 (2009) [http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 reprint]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[http://www.proteopedia.org/wiki/index.php/Image:Hab1.pdb Download the coordinates of Model 1 (PDB format)]

[[Image:hab1.pdb]]

[[Download the coordinates of Model 2 (PDB format)]]

[[Download the coordinates of Model 3 (PDB format)]]

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-09T23:20:51Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)</ref><ref>Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 (2006) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 reprint]</ref><ref>Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 (2007) [http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 reprint]</ref><ref>Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 (2009) [http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 reprint]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[http://www.proteopedia.org/wiki/index.php/Image:Hab1.pdb Download the coordinates of Model 1 (PDB format)]

[[Download the coordinates of Model 2 (PDB format)]]

[[Download the coordinates of Model 3 (PDB format)]]

References & Notes
<references/>

File:Hab1.pdb

2010-03-09T23:14:09Z

Yuan-Ping Pang: Model 1 of HAB•BoNTAe

Model 1 of HAB•BoNTAe

User:Yuan-Ping Pang/Sandbox 1

2010-03-09T22:49:50Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)</ref><ref>Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 (2006) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 reprint]</ref><ref>Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 (2007) [http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 reprint]</ref><ref>Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 (2009) [http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 reprint]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[[Download the coordinates of Model 1 (PDB format)]]

[[Download the coordinates of Model 2 (PDB format)]]

[[Download the coordinates of Model 3 (PDB format)]]

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-09T22:48:39Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)</ref><ref>Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 (2006) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 reprint]</ref><ref>Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 (2007) [http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 reprint]</ref><ref>Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 (2009) [http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 reprint]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[[Download the coordinates of Model 1 (PDB format)]]

[[Download the coordinates of Model 2 (PDB format)]]

[[Download the coordinates of Model 3 (PDB format)]]

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-09T22:38:46Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB - by Yuan-Ping Pang'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)</ref><ref>Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 (2006) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 reprint]</ref><ref>Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 (2007) [http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 reprint]</ref><ref>Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 (2009) [http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 reprint]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[[Download the coordinates of Model 1 (PDB format)]]

[[Download the coordinates of Model 2 (PDB format)]]

[[Download the coordinates of Model 3 (PDB format)]]

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-09T22:37:19Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Nanomolar Small-Molecule Inhibitor HAB - by Yuan-Ping Pang'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)</ref><ref>Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 (2006) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 reprint]</ref><ref>Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 (2007) [http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 reprint]</ref><ref>Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 (2009) [http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 reprint]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[[Download the coordinates of Model 1 (PDB format)]]

[[Download the coordinates of Model 2 (PDB format)]]

[[Download the coordinates of Model 3 (PDB format)]]

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-09T22:22:48Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Nanomolar Small-Molecule Inhibitor HAB - by Yuan-Ping Pang'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref>Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)</ref><ref>Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)</ref>. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 (2006) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 reprint]</ref><ref>Computer-Aided Lead Optimization: Improved Small-Molecule Inhibitor of the Zinc Endopeptidase of Botulinum Neurotoxin Serotype A, PLoS ONE 2:e761 (2007) [http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 reprint]</ref><ref>Potent New Small-Molecule Inhibitor of Botulinum Neurotoxin Serotype A Endopeptidase Developed by Synthesis-Based Computer-Aided Molecular Design, PLoS ONE 4:e7730 (2009) [http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 reprint]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[[Download the coordinates of Model 1 (PDB format)]]

[[Download the coordinates of Model 2 (PDB format)]]

[[Download the coordinates of Model 3 (PDB format)]]

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-09T22:12:06Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Nanomolar Small-Molecule Inhibitor HAB - by Yuan-Ping Pang'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg. Med. Chem., 14, 395-408 (2006) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 reprint]</ref><ref>Computer-Aided Lead Optimization: Improved Small-Molecule Inhibitor of the Zinc Endopeptidase of Botulinum Neurotoxin Serotype A, PLoS ONE, 2(8): e761 (2007) [http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 reprint]</ref><ref>Potent New Small-Molecule Inhibitor of Botulinum Neurotoxin Serotype A Endopeptidase Developed by Synthesis-Based Computer-Aided Molecular Design, PLoS ONE, 4(11): e7730 (2009) [http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 reprint]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[[Download the coordinates of Model 1 (PDB format)]]

[[Download the coordinates of Model 2 (PDB format)]]

[[Download the coordinates of Model 3 (PDB format)]]

References & Notes
<references/>

Proteopedia:Table of Contents

2010-03-09T22:05:48Z

Yuan-Ping Pang:

This guide to the contents of Proteopedia is maintained manually (not automatically generated) and so is inevitably incomplete. Please be sure to use the [[Help:Searching|search slots at the left]] if you don't find what you are looking for below.

<big>
{{#tree:id=siteTree|openlevels=1|close=top|open=top|

* Introduction to Structural Biology
** See [[About Macromolecular Structure]]
** Water

*** [[Water in macromolecular models|Water in Macromolecular Models]]
** Key Chemical Concepts for Structural Biology

*** [[Amino Acids]]
*** [[Cation-pi interactions]]
*** [[Hydrogen bond]]
*** [[Hydrogen in macromolecular models|Hydrogen in Macromolecular Models]]
*** [[Isoelectric point]]
*** [[Salt bridges]]

* Biomolecules
** [[About Macromolecular Structure]]

** Nucleotides, Nucleic Acids and Genetic Information
*** DNA
**** [[DNA]]
**** B-DNA [[1bna]]
**** [[Z-DNA]]

** Amino Acids
*** [[Amino Acids]]
*** [[Selenocysteine]]
** Proteins, Primary Structure
*** [[Conservation, Evolutionary]]
*** [[Isoelectric point]]

** Proteins, Three-Dimensional Structure
*** [[User:Tommie_Hata/Protein_Structure_Tutorial]]
*** [[S347/The four tiers of protein structure]]
*** [[Secondary structure]]
*** Protein structural motifs
**** [[User:James D Watson/Structural Templates]]
*** Fibrous Proteins
**** [[Coiled coil]]
**** [[Collagen]]
*** Protein Misfolding
**** [[Prion protein]]
**** [[A Physical Model of the Structure of GNNQQNY from Yeast Prion Sup35]]

** Colored Proteins & those that Change Color
*** [[Green Fluorescent Protein]]; [[GFP (Hebrew)]]
*** [[Dronpa]]
*** [[Factor IX]]

** DNA Binding Proteins
*** [[Helix-turn-helix motif]]
*** [[DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1]]

** Protein Function: Myoglobin and Hemoglobin, Muscle Contraction, and Antibodies
*** Antibodies
**** [[IgA]]
**** [[Epitopes]]
**** [[Major Histocompatibility Complex Class I]]
*** [[Calmodulin in motion]]
*** [[Myoglobin]]
*** [[Hemoglobin]]; [[Hemoglobin (Hebrew)]]
*** [[Kinesin-5]]
** Lipids and Biological Membranes
** Lipid Binding Proteins
*** [[CRABP I ( Cellular Retinoic Acid Binding Protein )]]
** Membrane Transport Proteins
*** [[A Physical Model of the β2-Adrenergic Receptor]]
*** [[Lactose Permease]]
*** [[Proton Channels]]
*** [[Ion channels]]
**** [[M2 Proton Channel]]
**** [[Voltage-gated calcium channels]]
*** [[Mechanosensitive channels: opening and closing]]
***[[Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System]]

** Prions and Intrinsically Disordered Proteins
*** [[Prion protein]]
*** [[Doppel]]
*** [[Intrinsically Disordered Protein]]

** Toxins
*** [[Insecticidal delta-endotoxin Cyt2Ba from Bacillus thuringiensis]]

** Mitosis, Meiosis and Cargo Transport Proteins
*** [[Kinesin-5]]

** Viruses
*** [[User:Wayne Decatur/Suppression of RNA Silencing by Viruses]]
*** Filamentous bacteriphage
**** [[G3p]] - minor coat protein found on the surface of filamentous bacteriophage
*** HIV
**** [[HIV-1 protease]]
**** [[HIV-1 Gag]]
**** [[HIV-1 Gag Recruitment of Tsg101 and the Viral Budding Process]]
**** [[User:Eric Martz/Molecular Playground/HIVDrug]]
*** Herpes Simplex Virus
**** [[Herpes Simplex Virus Thymidine Kinase]]
*** Influenza
**** [[Influenza hemagglutinin]]
**** [[Avian Influenza Neuraminidase, Tamiflu and Relenza]]

* Enzymes
** Enzymatic Catalysis
*** Acid-beta-glucosidase
**** reHuman Acid-beta-glucosidase made in CHO cells [[1ogs]]
**** reHuman Acid-beta-glucosidase made in CHO cells bound to conduritol B epoxide [[1y7v]]
**** reHuman Acid-beta-glucosidase made in carrot cells complexed with N-butyl-deoxynojirimycin [[2v3d]]
**** Velaglucerase Alfa [[2wkl]]
*** Acid Proteases
**** [[HIV-1 protease]]

**** [[Streptomyces griseus Aminopeptidase (SGAP)]]; [[Aminopeptidase]]
*** [[Aconitase]]
*** Cysteine Proteases
*** [[Hen Egg-White (HEW) Lysozyme]]
*** [[Choline Oxidase]]
*** [[Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System]]
*** [[Metalloproteases]]
**** [[Matrix metalloproteinases]]
*** Oxidoreductases
**** [[NADH quinone oxidoreductase ]]
*** [[Phosphofructokinase %28PFK%29]]
*** [[Pyruvate phosphate dikinase]]
*** [[Serotonin N-acetyltransferase]]
*** Serine Hydrolases
**** [[Acetylcholinesterase]] (AChE)
***** [[Acetylcholine]]
***** [[Flexibility of aromatic residues in acetylcholinesterase]]
***** [[AChE inhibitors and substrates]]
****** [[1eve]] AChE-Aricept complex; [[1eve (Arabic)]]; [[1eve (Chinese)]]; [[1eve (Italian)]]; [[1eve (Russian)]]; [[1eve (Spanish)]]; [[1eve (Turkish)]]
****** [[AChE bivalent inhibitors]]
**** [[Tobacco Etch Virus (TEV) Protease]]
*** [[Serine Protease]]
**** [[Trypsin]]
*** [[Triose Phosphate Isomerase]]
** Enzyme Inhibitors
*** [[Alpha-1-antitrypsin]]
** Enzyme Kinetics, Inhibition, and Control
***[[Avian Influenza Neuraminidase, Tamiflu and Relenza]]
** Biochemical Signaling
*** [[Nitric oxide synthase]], [[NOS structures]]
*** [[Recoverin, a calcium-activated myristoyl switch]]
*** [[Bcl-2]]
*** [[C-Myc]]
*** [[C-di-GMP signaling]]

** Enzymes - Molecular Machines
*** [[Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System]]
*** [[Pyruvate phosphate dikinase]]

* Metabolism
** Introduction to Metabolism

** Glucose Catabolism
*** [[Triose Phosphate Isomerase]]
***[[Phosphofructokinase %28PFK%29]]

** Glycogen Metabolism and Gluconeogenesis
*** [[Phosphoglucose isomerase]]
*** [[Calmodulin in motion]]
*** [[Biotin Protein Ligase]]

** Citric Acid Cycle
*** [[Aconitase]]

** Electron Transport and Oxidative Phosphorylation
*** [[NADH quinone oxidoreductase ]]

** Photosynthesis
*** [[Photosystem II]]
*** [[Ribulose-1,5-bisphosphate carboxylase/oxygenase]]
*** [[PrrA in Rhodobacter sphaeroides]]
*** [[Pyruvate phosphate dikinase]]

** Lipid Metabolism
*** [[Acid-beta-glucosidase]]
** Amino Acid Metabolism
*** [[Aromatic amino acid hydroxylases]]
*** [[Phenylalanine hydroxylase]]
*** [[Tyrosine hydroxylase]]
*** [[ATP Phosphoribosyl Transferase]]
*** [[Isochorismate pyruvate lyase]]
** Mammalian Fuel Metabolism: Integration and Regulation
** Nucleotide Metabolism
*** [[Dihydrofolate reductase]]

* Gene Expression and Replication

** Nucleic Acid Structure
*** [[DNA]]
**** B-DNA [[1bna]]
**** [[Z-DNA]]
*** [[Nucleosomes]]

** DNA Replication, Repair, and Recombination
*** [[DNA Replication,Transcription and Translation]]
*** [[DNA Polymerase I]]
*** [[PcrA helicase]]
*** [[Fpg Nei Protein Superfamily]] - DNA Repair and Base Excision DNA Repair
*** [[Human RecQ-Like protein 1]] - RecQ family of DNA helicases are conserved in from bacteria to man
*** [[Structure of E. coli DnaC helicase loader]]
***[[1x9n#Crystal Structure of Human DNA Ligase I bound to 5.27-adenylated.2C nicked DNA]]
*** [[Rop protein]]

** Transcription and RNA Processing
*** [[C-Myc]]
*** [[Lac repressor]]
*** [[Reverse transcriptase]]
*** [[TATA-Binding Protein]]
*** [[RSP1275]]
*** [[Transcription Termination Factor Rho]]

** Protein Synthesis
*** [[Ribosome]]
*** [[SelB Recognition]]
** Regulation of Gene Expression
*** [[Lac repressor]]
*** [[Irr]] (Iron Response Regulator )
*** Oncogenes
**** [[P53]]
**** [[SRC]]
*** [[Tangible Models of Cdc42 Interacting With Intersectin]]

* Evolution
** [[Conservation, Evolutionary]]

** [[Extremophiles]]

* Immune System
** Antibodies
*** [[IgA]]
*** [[Epitopes]]
** [[Major Histocompatibility Complex Class I]]
*** [[Human beta two microglobulin]]

* Diseases
** Cancer
*** [[SRC]]
*** [[Proteins involved in cancer]]

* Methods of Structure Determination
** X-ray
*** [[X-ray crystallography]]
**** [[Asymmetric Unit]]
**** [[Biological Unit]]
**** [[Electron density maps]]
*** SAXS
** NMR
*** [[NMR Ensembles of Models]]
** Electron Microscopy

* Methods of Structure & Sequence Analysis
** Structural Analysis & Visualization
*** [[CPK]] - Corey-Pauling-Koltun spacefilling molecular models and color scheme for elements
*** [[Chime]]
*** Jmol
**** [[S347/Visualising protein structure|Visualising Protein Structure]] - Introduction to Jmol
**** [[FirstGlance in Jmol]]
*** [[User:Wayne Decatur/Teaching Proteopedia|Teaching Proteopedia]]
*** [[User:Wayne Decatur/Generate Unfolded Structures|Generate Unfolded Structures]]
*** Homology Model
**** [[User:Wayne Decatur/Homology Modeling|Homology Modeling]]
**** [[User:Emi Nakayama/TRIM5a Homology Models|TRIM5a Homology Models]] - Differences in models as a function of their templates
*** [[DRuMS]] - set of standard color schemes for macromolecular visualization

** Sequence Analysis
*** [[User:Wayne Decatur/Sequence analysis tools|Sequence Analysis Tools]]

* Model Structures
** See [[Theoretical models]]
** [[African Malaria Mosquito Acetylcholinesterase]]
** [[Structure of E. coli DnaC helicase loader]]

* Miscellaneous
** [[Molecular Playground]]
** [[Research Groups]]
}}
</big>

Proteopedia:Table of Contents

2010-03-09T22:03:50Z

Yuan-Ping Pang:

This guide to the contents of Proteopedia is maintained manually (not automatically generated) and so is inevitably incomplete. Please be sure to use the [[Help:Searching|search slots at the left]] if you don't find what you are looking for below.

<big>
{{#tree:id=siteTree|openlevels=1|close=top|open=top|

* Introduction to Structural Biology
** See [[About Macromolecular Structure]]
** Water

*** [[Water in macromolecular models|Water in Macromolecular Models]]
** Key Chemical Concepts for Structural Biology

*** [[Amino Acids]]
*** [[Cation-pi interactions]]
*** [[Hydrogen bond]]
*** [[Hydrogen in macromolecular models|Hydrogen in Macromolecular Models]]
*** [[Isoelectric point]]
*** [[Salt bridges]]

* Biomolecules
** [[About Macromolecular Structure]]

** Nucleotides, Nucleic Acids and Genetic Information
*** DNA
**** [[DNA]]
**** B-DNA [[1bna]]
**** [[Z-DNA]]

** Amino Acids
*** [[Amino Acids]]
*** [[Selenocysteine]]
** Proteins, Primary Structure
*** [[Conservation, Evolutionary]]
*** [[Isoelectric point]]

** Proteins, Three-Dimensional Structure
*** [[User:Tommie_Hata/Protein_Structure_Tutorial]]
*** [[S347/The four tiers of protein structure]]
*** [[Secondary structure]]
*** Protein structural motifs
**** [[User:James D Watson/Structural Templates]]
*** Fibrous Proteins
**** [[Coiled coil]]
**** [[Collagen]]
*** Protein Misfolding
**** [[Prion protein]]
**** [[A Physical Model of the Structure of GNNQQNY from Yeast Prion Sup35]]

** Colored Proteins & those that Change Color
*** [[Green Fluorescent Protein]]; [[GFP (Hebrew)]]
*** [[Dronpa]]
*** [[Factor IX]]

** DNA Binding Proteins
*** [[Helix-turn-helix motif]]
*** [[DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1]]

** Protein Function: Myoglobin and Hemoglobin, Muscle Contraction, and Antibodies
*** Antibodies
**** [[IgA]]
**** [[Epitopes]]
**** [[Major Histocompatibility Complex Class I]]
*** [[Calmodulin in motion]]
*** [[Myoglobin]]
*** [[Hemoglobin]]; [[Hemoglobin (Hebrew)]]
*** [[Kinesin-5]]
** Lipids and Biological Membranes
** Lipid Binding Proteins
*** [[CRABP I ( Cellular Retinoic Acid Binding Protein )]]
** Membrane Transport Proteins
*** [[A Physical Model of the β2-Adrenergic Receptor]]
*** [[Lactose Permease]]
*** [[Proton Channels]]
*** [[Ion channels]]
**** [[M2 Proton Channel]]
**** [[Voltage-gated calcium channels]]
*** [[Mechanosensitive channels: opening and closing]]
***[[Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System]]

** Prions and Intrinsically Disordered Proteins
*** [[Prion protein]]
*** [[Doppel]]
*** [[Intrinsically Disordered Protein]]

** Toxins
*** [[Insecticidal delta-endotoxin Cyt2Ba from Bacillus thuringiensis]]
*** [[Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB]]

** Mitosis, Meiosis and Cargo Transport Proteins
*** [[Kinesin-5]]

** Viruses
*** [[User:Wayne Decatur/Suppression of RNA Silencing by Viruses]]
*** Filamentous bacteriphage
**** [[G3p]] - minor coat protein found on the surface of filamentous bacteriophage
*** HIV
**** [[HIV-1 protease]]
**** [[HIV-1 Gag]]
**** [[HIV-1 Gag Recruitment of Tsg101 and the Viral Budding Process]]
**** [[User:Eric Martz/Molecular Playground/HIVDrug]]
*** Herpes Simplex Virus
**** [[Herpes Simplex Virus Thymidine Kinase]]
*** Influenza
**** [[Influenza hemagglutinin]]
**** [[Avian Influenza Neuraminidase, Tamiflu and Relenza]]

* Enzymes
** Enzymatic Catalysis
*** Acid-beta-glucosidase
**** reHuman Acid-beta-glucosidase made in CHO cells [[1ogs]]
**** reHuman Acid-beta-glucosidase made in CHO cells bound to conduritol B epoxide [[1y7v]]
**** reHuman Acid-beta-glucosidase made in carrot cells complexed with N-butyl-deoxynojirimycin [[2v3d]]
**** Velaglucerase Alfa [[2wkl]]
*** Acid Proteases
**** [[HIV-1 protease]]

**** [[Streptomyces griseus Aminopeptidase (SGAP)]]; [[Aminopeptidase]]
*** [[Aconitase]]
*** Cysteine Proteases
*** [[Hen Egg-White (HEW) Lysozyme]]
*** [[Choline Oxidase]]
*** [[Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System]]
*** [[Metalloproteases]]
**** [[Matrix metalloproteinases]]
*** Oxidoreductases
**** [[NADH quinone oxidoreductase ]]
*** [[Phosphofructokinase %28PFK%29]]
*** [[Pyruvate phosphate dikinase]]
*** [[Serotonin N-acetyltransferase]]
*** Serine Hydrolases
**** [[Acetylcholinesterase]] (AChE)
***** [[Acetylcholine]]
***** [[Flexibility of aromatic residues in acetylcholinesterase]]
***** [[AChE inhibitors and substrates]]
****** [[1eve]] AChE-Aricept complex; [[1eve (Arabic)]]; [[1eve (Chinese)]]; [[1eve (Italian)]]; [[1eve (Russian)]]; [[1eve (Spanish)]]; [[1eve (Turkish)]]
****** [[AChE bivalent inhibitors]]
**** [[Tobacco Etch Virus (TEV) Protease]]
*** [[Serine Protease]]
**** [[Trypsin]]
*** [[Triose Phosphate Isomerase]]
** Enzyme Inhibitors
*** [[Alpha-1-antitrypsin]]
*** [[Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB]]
** Enzyme Kinetics, Inhibition, and Control
***[[Avian Influenza Neuraminidase, Tamiflu and Relenza]]
** Biochemical Signaling
*** [[Nitric oxide synthase]], [[NOS structures]]
*** [[Recoverin, a calcium-activated myristoyl switch]]
*** [[Bcl-2]]
*** [[C-Myc]]
*** [[C-di-GMP signaling]]

** Enzymes - Molecular Machines
*** [[Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System]]
*** [[Pyruvate phosphate dikinase]]

* Metabolism
** Introduction to Metabolism

** Glucose Catabolism
*** [[Triose Phosphate Isomerase]]
***[[Phosphofructokinase %28PFK%29]]

** Glycogen Metabolism and Gluconeogenesis
*** [[Phosphoglucose isomerase]]
*** [[Calmodulin in motion]]
*** [[Biotin Protein Ligase]]

** Citric Acid Cycle
*** [[Aconitase]]

** Electron Transport and Oxidative Phosphorylation
*** [[NADH quinone oxidoreductase ]]

** Photosynthesis
*** [[Photosystem II]]
*** [[Ribulose-1,5-bisphosphate carboxylase/oxygenase]]
*** [[PrrA in Rhodobacter sphaeroides]]
*** [[Pyruvate phosphate dikinase]]

** Lipid Metabolism
*** [[Acid-beta-glucosidase]]
** Amino Acid Metabolism
*** [[Aromatic amino acid hydroxylases]]
*** [[Phenylalanine hydroxylase]]
*** [[Tyrosine hydroxylase]]
*** [[ATP Phosphoribosyl Transferase]]
*** [[Isochorismate pyruvate lyase]]
** Mammalian Fuel Metabolism: Integration and Regulation
** Nucleotide Metabolism
*** [[Dihydrofolate reductase]]

* Gene Expression and Replication

** Nucleic Acid Structure
*** [[DNA]]
**** B-DNA [[1bna]]
**** [[Z-DNA]]
*** [[Nucleosomes]]

** DNA Replication, Repair, and Recombination
*** [[DNA Replication,Transcription and Translation]]
*** [[DNA Polymerase I]]
*** [[PcrA helicase]]
*** [[Fpg Nei Protein Superfamily]] - DNA Repair and Base Excision DNA Repair
*** [[Human RecQ-Like protein 1]] - RecQ family of DNA helicases are conserved in from bacteria to man
*** [[Structure of E. coli DnaC helicase loader]]
***[[1x9n#Crystal Structure of Human DNA Ligase I bound to 5.27-adenylated.2C nicked DNA]]
*** [[Rop protein]]

** Transcription and RNA Processing
*** [[C-Myc]]
*** [[Lac repressor]]
*** [[Reverse transcriptase]]
*** [[TATA-Binding Protein]]
*** [[RSP1275]]
*** [[Transcription Termination Factor Rho]]

** Protein Synthesis
*** [[Ribosome]]
*** [[SelB Recognition]]
** Regulation of Gene Expression
*** [[Lac repressor]]
*** [[Irr]] (Iron Response Regulator )
*** Oncogenes
**** [[P53]]
**** [[SRC]]
*** [[Tangible Models of Cdc42 Interacting With Intersectin]]

* Evolution
** [[Conservation, Evolutionary]]

** [[Extremophiles]]

* Immune System
** Antibodies
*** [[IgA]]
*** [[Epitopes]]
** [[Major Histocompatibility Complex Class I]]
*** [[Human beta two microglobulin]]

* Diseases
** Cancer
*** [[SRC]]
*** [[Proteins involved in cancer]]

* Methods of Structure Determination
** X-ray
*** [[X-ray crystallography]]
**** [[Asymmetric Unit]]
**** [[Biological Unit]]
**** [[Electron density maps]]
*** SAXS
** NMR
*** [[NMR Ensembles of Models]]
** Electron Microscopy

* Methods of Structure & Sequence Analysis
** Structural Analysis & Visualization
*** [[CPK]] - Corey-Pauling-Koltun spacefilling molecular models and color scheme for elements
*** [[Chime]]
*** Jmol
**** [[S347/Visualising protein structure|Visualising Protein Structure]] - Introduction to Jmol
**** [[FirstGlance in Jmol]]
*** [[User:Wayne Decatur/Teaching Proteopedia|Teaching Proteopedia]]
*** [[User:Wayne Decatur/Generate Unfolded Structures|Generate Unfolded Structures]]
*** Homology Model
**** [[User:Wayne Decatur/Homology Modeling|Homology Modeling]]
**** [[User:Emi Nakayama/TRIM5a Homology Models|TRIM5a Homology Models]] - Differences in models as a function of their templates
*** [[DRuMS]] - set of standard color schemes for macromolecular visualization

** Sequence Analysis
*** [[User:Wayne Decatur/Sequence analysis tools|Sequence Analysis Tools]]

* Model Structures
** See [[Theoretical models]]
** [[African Malaria Mosquito Acetylcholinesterase]]
** [[Structure of E. coli DnaC helicase loader]]
** [[Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB]]

* Miscellaneous
** [[Molecular Playground]]
** [[Research Groups]]
}}
</big>

User:Yuan-Ping Pang/Sandbox 1

2010-03-09T21:49:48Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Nanomolar Small-Molecule Inhibitor HAB - by Yuan-Ping Pang'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg. Med. Chem., 14, 395-408 (2006) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 reprint]</ref><ref>Computer-Aided Lead Optimization: Improved Small-Molecule Inhibitor of the Zinc Endopeptidase of Botulinum Neurotoxin Serotype A, PLoS ONE, 2(8): e761 (2007) [http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 reprint]</ref><ref>Potent New Small-Molecule Inhibitor of Botulinum Neurotoxin Serotype A Endopeptidase Developed by Synthesis-Based Computer-Aided Molecular Design, PLoS ONE, 4(11): e7730 (2009) [http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 reprint]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are released in the models below<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[[Download the coordinates of Model 1 (PDB format)]]

[[Download the coordinates of Model 2 (PDB format)]]

[[Download the coordinates of Model 3 (PDB format)]]

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-09T21:47:55Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Nanomolar Small-Molecule Inhibitor HAB - by Yuan-Ping Pang'''

Botulinum neurotoxin serotype A (BoNTA) causes botulism. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg. Med. Chem., 14, 395-408 (2006) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 reprint]</ref><ref>Computer-Aided Lead Optimization: Improved Small-Molecule Inhibitor of the Zinc Endopeptidase of Botulinum Neurotoxin Serotype A, PLoS ONE, 2(8): e761 (2007) [http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 reprint]</ref><ref>Potent New Small-Molecule Inhibitor of Botulinum Neurotoxin Serotype A Endopeptidase Developed by Synthesis-Based Computer-Aided Molecular Design, PLoS ONE, 4(11): e7730 (2009) [http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 reprint]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 20.8%, 13.4% and 11.9%, respectively. To evaluate the computational methods, the coordinates of the three models are released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are released in the models below<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[[Download the coordinates of Model 1 (PDB format)]]

[[Download the coordinates of Model 2 (PDB format)]]

[[Download the coordinates of Model 3 (PDB format)]]

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-09T21:47:16Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Nanomolar Small-Molecule Inhibitor HAB - by Yuan-Ping Pang'''

Botulinum neurotoxin serotype A (BoNTA) causes a life-threatening neuroparalytic disease known as botulism. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg. Med. Chem., 14, 395-408 (2006) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 reprint]</ref><ref>Computer-Aided Lead Optimization: Improved Small-Molecule Inhibitor of the Zinc Endopeptidase of Botulinum Neurotoxin Serotype A, PLoS ONE, 2(8): e761 (2007) [http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 reprint]</ref><ref>Potent New Small-Molecule Inhibitor of Botulinum Neurotoxin Serotype A Endopeptidase Developed by Synthesis-Based Computer-Aided Molecular Design, PLoS ONE, 4(11): e7730 (2009) [http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 reprint]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 20.8%, 13.4% and 11.9%, respectively. To evaluate the computational methods, the coordinates of the three models are released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are released in the models below<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[[Download the coordinates of Model 1 (PDB format)]]

[[Download the coordinates of Model 2 (PDB format)]]

[[Download the coordinates of Model 3 (PDB format)]]

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-09T21:44:54Z

Yuan-Ping Pang:

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Nanomolar Small-Molecule Inhibitor HAB - by Yuan-Ping Pang'''

Botulinum neurotoxin serotype A (BoNTA) causes a life-threatening neuroparalytic disease known as botulism. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg. Med. Chem., 14, 395-408 (2006) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF8-4H7TCVW-2&_user=130561&_coverDate=01/15/2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000010878&_version=1&_urlVersion=0&_userid=130561&md5=a7d96c458cd0ce9f3bb466ab3e6c9692 reprint]</ref><ref>Computer-Aided Lead Optimization: Improved Small-Molecule Inhibitor of the Zinc Endopeptidase of Botulinum Neurotoxin Serotype A, PLoS ONE, 2(8): e761 (2007) [http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi/10.1371/journal.pone.0000761 reprint]</ref><ref>Potent New Small-Molecule Inhibitor of Botulinum Neurotoxin Serotype A Endopeptidase Developed by Synthesis-Based Computer-Aided Molecular Design, PLoS ONE, 4(11): e7730 (2009) [http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0007730 reprint]</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 20.8%, 13.4% and 11.9%, respectively. To evaluate the computational methods, the coordinates of the three models are released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are released in the models below<ref>The models of HAB•BoNTAe were released at [http://mayoresearch.mayo.edu/mayo/research/camdl/protein-structure-prediction.cfm Mayo Research Protein Structure Prediction] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[[Download the coordinates of Model 1 (PDB format)]]

[[Download the coordinates of Model 2 (PDB format)]]

[[Download the coordinates of Model 3 (PDB format)]]

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-09T21:23:37Z

Yuan-Ping Pang: HAB-BoNTAe

{{Theoretical_model}}

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Nanomolar Small-Molecule Inhibitor HAB - by Yuan-Ping Pang'''

Botulinum neurotoxin serotype A (BoNTA) causes a life-threatening neuroparalytic disease known as botulism. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA<ref>Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg. Med. Chem., 14, 395-408 (2006)</ref><ref>Computer-Aided Lead Optimization: Improved Small-Molecule Inhibitor of the Zinc Endopeptidase of Botulinum Neurotoxin Serotype A, PLoS ONE, 2(8): e761 (2007).</ref><ref>Potent New Small-Molecule Inhibitor of Botulinum Neurotoxin Serotype A Endopeptidase Developed by Synthesis-Based Computer-Aided Molecular Design, PLoS ONE, 4(11): e7730 (2009).</ref>. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 20.8%, 13.4% and 11.9%, respectively. To evaluate the computational methods, the coordinates of the three models are released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are released in the models below<ref>The models of HAB•BoNTAe were released at [[Mayo Research Protein Structure Prediction]] on March 5, 2010.</ref>. The full structure of HAB will be released upon manuscript acceptance<ref>This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.</ref>.

[[Download the coordinates of Model 1 (PDB format)]]

[[Download the coordinates of Model 2 (PDB format)]]

[[Download the coordinates of Model 3 (PDB format)]]

References & Notes
<references/>

User:Yuan-Ping Pang/Sandbox 1

2010-03-09T20:30:03Z

Yuan-Ping Pang:

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Nanomolar Small-Molecule Inhibitor HAB - by Yuan-Ping Pang'''

----

Botulinum neurotoxin serotype A (BoNTA) causes a life-threatening neuroparalytic disease known as botulism. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA <ref>Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A</ref>. HAB (to be published) is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe and has a functional group coordinating the zinc divalent cation embedded in the active site of BoNTAe according to the simulations using the cationic dummy atom approach [refs]. Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 20.8%, 13.4% and 11.9%, respectively. To evaluate the computational methods, the coordinates of the three models are released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are released in the models below. The full structure of HAB will be released upon manuscript acceptance.

[[Download the coordinates of Model 1 (PDB format)]]

[[Download the coordinates of Model 2 (PDB format)]]

[[Download the coordinates of Model 3 (PDB format)]]

'''References & Notes'''

1. The models of HAB•BoNTAe were released at [[Mayo Research Protein Structure Prediction]] on March 5, 2010.

2. This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.

User:Yuan-Ping Pang/Sandbox 1

2010-03-09T20:10:51Z

Yuan-Ping Pang:

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Nanomolar Small-Molecule Inhibitor HAB - by Yuan-Ping Pang'''

----

Botulinum neurotoxin serotype A (BoNTA) causes a life-threatening neuroparalytic disease known as botulism. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA [refs]. HAB (to be published) is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe and has a functional group coordinating the zinc divalent cation embedded in the active site of BoNTAe according to the simulations using the cationic dummy atom approach [refs]. Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 20.8%, 13.4% and 11.9%, respectively. To evaluate the computational methods, the coordinates of the three models are released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are released in the models below. The full structure of HAB will be released upon manuscript acceptance.

[[Download the coordinates of Model1 (PDB format)]]

[[Download the coordinates of Model2 (PDB format)]]

[[Download the coordinates of Model3 (PDB format)]]

'''References & Notes'''

User:Yuan-Ping Pang/Sandbox 1

2010-03-09T19:19:00Z

Yuan-Ping Pang:

'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Nanomolar Small-Molecule Inhibitor HAB - by YP Pang'''

----

Botulinum neurotoxin serotype A (BoNTA) causes a life-threatening neuroparalytic disease known as botulism. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as antidotes to antagonize the extracellular or intracellular toxin [refs]. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group is highly flexible; the percentages of the top three most-populated conformations of the complex (models 1-3) are 20.8%, 13.4% and 11.9%, respectively. The coordinates of the three models are released before the forthcoming crystal structure of HAB•BoNTAe. Only 60% of the heavy atoms of HAB are released in the models below. The full structure of HAB will be released upon manuscript acceptance.

User:Yuan-Ping Pang/Sandbox 1

2010-03-09T03:42:39Z

Yuan-Ping Pang: New page: This is a test.

This is a test.

User:Yuan-Ping Pang

2010-03-09T03:41:10Z

Yuan-Ping Pang:

*[[User: Yuan-Ping Pang/Sandbox 1]]

Talk:Pikaart Sandbox

2010-03-08T22:56:01Z

Yuan-Ping Pang: Talk:Sandbox moved to Talk:Sandbox-test: test

#REDIRECT [[Talk:Sandbox-test]]

Talk:Biotin binding Avidin

2010-03-08T22:56:01Z

Yuan-Ping Pang: Talk:Sandbox moved to Talk:Sandbox-test: test

Hellow world