User:Yuan-Ping Pang/Sandbox 1 - Revision history

http://52.214.119.220/wiki/index.php?action=history&feed=atom&title=User%3AYuan-Ping_Pang%2FSandbox_1 User:Yuan-Ping Pang/Sandbox 1 - Revision history 2026-04-15T22:53:01Z Revision history for this page on the wiki MediaWiki 1.11.2 http://52.214.119.220/wiki/index.php?title=User:Yuan-Ping_Pang/Sandbox_1&diff=1055630&oldid=prev Yuan-Ping Pang: Replacing page with 'This is a test.' 2010-03-11T04:28:34Z

<p>Replacing page with 'This is a test.'</p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 04:28, 11 March 2010</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">{{Theoretical_model}}</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">This is </ins>a <ins style="color: red; font-weight: bold; text-decoration: none;">test</ins>.</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with </del>a <del style="color: red; font-weight: bold; text-decoration: none;">Small-Molecule Inhibitor HAB'''</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">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>.</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">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</del>.<del style="color: red; font-weight: bold; text-decoration: none;">pdb)] (PDB format)</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">References & Notes</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"><references/></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr> </table>

Yuan-Ping Pang http://52.214.119.220/wiki/index.php?title=User:Yuan-Ping_Pang/Sandbox_1&diff=1055625&oldid=prev Yuan-Ping Pang at 03:54, 11 March 2010 2010-03-11T03:54:38Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 03:54, 11 March 2010</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 4:</td> <td colspan="2" class="diff-lineno">Line 4:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>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>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>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 <ins style="color: red; font-weight: bold; text-decoration: none;">used </ins>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>.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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)</div></td></tr> </table>

Yuan-Ping Pang http://52.214.119.220/wiki/index.php?title=User:Yuan-Ping_Pang/Sandbox_1&diff=1055624&oldid=prev Yuan-Ping Pang at 03:53, 11 March 2010 2010-03-11T03:53:01Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 03:53, 11 March 2010</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 4:</td> <td colspan="2" class="diff-lineno">Line 4:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>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>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>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 <ins style="color: red; font-weight: bold; text-decoration: none;">the accuracy of </ins>the computational methods <ins style="color: red; font-weight: bold; text-decoration: none;">for generating HAB•BoNTAe</ins>, 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>.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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)</div></td></tr> </table>

Yuan-Ping Pang http://52.214.119.220/wiki/index.php?title=User:Yuan-Ping_Pang/Sandbox_1&diff=1055623&oldid=prev Yuan-Ping Pang at 03:46, 11 March 2010 2010-03-11T03:46:18Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 03:46, 11 March 2010</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 4:</td> <td colspan="2" class="diff-lineno">Line 4:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>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 <del style="color: red; font-weight: bold; text-decoration: none;">(</del>1998<del style="color: red; font-weight: bold; text-decoration: none;">)</del>]</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 <del style="color: red; font-weight: bold; text-decoration: none;">(</del>2001<del style="color: red; font-weight: bold; text-decoration: none;">)</del>]</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>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>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>.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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)</div></td></tr> </table>

Yuan-Ping Pang http://52.214.119.220/wiki/index.php?title=User:Yuan-Ping_Pang/Sandbox_1&diff=1055622&oldid=prev Yuan-Ping Pang at 03:45, 11 March 2010 2010-03-11T03:45:14Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 03:45, 11 March 2010</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 4:</td> <td colspan="2" class="diff-lineno">Line 4:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>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 <del style="color: red; font-weight: bold; text-decoration: none;">(</del>2006<del style="color: red; font-weight: bold; text-decoration: none;">)</del>]</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 <del style="color: red; font-weight: bold; text-decoration: none;">(</del>2007<del style="color: red; font-weight: bold; text-decoration: none;">)</del>]</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 <del style="color: red; font-weight: bold; text-decoration: none;">(</del>2009<del style="color: red; font-weight: bold; text-decoration: none;">)</del>]</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>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>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)<ins style="color: red; font-weight: bold; text-decoration: none;">]</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</ins>]</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>.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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)</div></td></tr> </table>

Yuan-Ping Pang http://52.214.119.220/wiki/index.php?title=User:Yuan-Ping_Pang/Sandbox_1&diff=1053907&oldid=prev Yuan-Ping Pang at 01:28, 10 March 2010 2010-03-10T01:28:38Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 01:28, 10 March 2010</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 6:</td> <td colspan="2" class="diff-lineno">Line 6:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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>.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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>.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Download the coordinates of [http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb <del style="color: red; font-weight: bold; text-decoration: none;">Model </del>1 (Hab1.pdb)], [http://www.proteopedia.org/wiki/images/f/f7/Hab2.pdb <del style="color: red; font-weight: bold; text-decoration: none;">Model </del>2 (Hab2.pdb)], and [http://www.proteopedia.org/wiki/images/5/59/Hab3.pdb <del style="color: red; font-weight: bold; text-decoration: none;">Model </del>3 (Hab3.pdb)] (PDB format)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Download the coordinates of <ins style="color: red; font-weight: bold; text-decoration: none;">Models </ins>[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)</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>References & Notes</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>References & Notes</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><references/></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><references/></div></td></tr> </table>

Yuan-Ping Pang http://52.214.119.220/wiki/index.php?title=User:Yuan-Ping_Pang/Sandbox_1&diff=1053906&oldid=prev Yuan-Ping Pang at 01:27, 10 March 2010 2010-03-10T01:27:12Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 01:27, 10 March 2010</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 6:</td> <td colspan="2" class="diff-lineno">Line 6:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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>.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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>.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>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)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Download the coordinates of [http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb Model 1 (Hab1.pdb)]<ins style="color: red; font-weight: bold; text-decoration: none;">, </ins>[http://www.proteopedia.org/wiki/images/f/f7/Hab2.pdb Model 2 (Hab2.pdb)]<ins style="color: red; font-weight: bold; text-decoration: none;">, and </ins>[http://www.proteopedia.org/wiki/images/5/59/Hab3.pdb Model 3 (Hab3.pdb)] (PDB format)</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>References & Notes</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>References & Notes</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><references/></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><references/></div></td></tr> </table>

Yuan-Ping Pang http://52.214.119.220/wiki/index.php?title=User:Yuan-Ping_Pang/Sandbox_1&diff=1053905&oldid=prev Yuan-Ping Pang at 01:25, 10 March 2010 2010-03-10T01:25:49Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 01:25, 10 March 2010</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 6:</td> <td colspan="2" class="diff-lineno">Line 6:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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>.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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>.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb <del style="color: red; font-weight: bold; text-decoration: none;">Download the coordinates of </del>Model 1 (Hab1.pdb<del style="color: red; font-weight: bold; text-decoration: none;">, PDB format</del>)]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Download the coordinates of </ins>[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<ins style="color: red; font-weight: bold; text-decoration: none;">)] (</ins>PDB format)</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[http://www.proteopedia.org/wiki/images/f/f7/Hab2.pdb <del style="color: red; font-weight: bold; text-decoration: none;">Download the coordinates of </del>Model 2 (Hab2.pdb<del style="color: red; font-weight: bold; text-decoration: none;">, PDB format</del>)]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[http://www.proteopedia.org/wiki/images/5/59/Hab3.pdb <del style="color: red; font-weight: bold; text-decoration: none;">Download the coordinates of </del>Model 3 (Hab3.pdb<del style="color: red; font-weight: bold; text-decoration: none;">, </del>PDB format)<del style="color: red; font-weight: bold; text-decoration: none;">]</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>References & Notes</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>References & Notes</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><references/></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><references/></div></td></tr> </table>

Yuan-Ping Pang http://52.214.119.220/wiki/index.php?title=User:Yuan-Ping_Pang/Sandbox_1&diff=1053904&oldid=prev Yuan-Ping Pang at 01:21, 10 March 2010 2010-03-10T01:21:43Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 01:21, 10 March 2010</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 4:</td> <td colspan="2" class="diff-lineno">Line 4:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>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>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>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><ins style="color: red; font-weight: bold; text-decoration: none;">[http://ovidsp.tx.ovid.com/sp-2.3/ovidweb.cgi?&S=IMDCFPMAJEDDJGMPNCELMGJLLMPLAA00&Link+Set=S.sh.15.16.19.40%7c35%7csl_10 </ins>Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)<ins style="color: red; font-weight: bold; text-decoration: none;">]</ins></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>.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb Download the coordinates of Model 1 (Hab1.pdb, PDB format)]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb Download the coordinates of Model 1 (Hab1.pdb, PDB format)]</div></td></tr> </table>

Yuan-Ping Pang http://52.214.119.220/wiki/index.php?title=User:Yuan-Ping_Pang/Sandbox_1&diff=1053903&oldid=prev Yuan-Ping Pang at 01:19, 10 March 2010 2010-03-10T01:19:04Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 01:19, 10 March 2010</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 4:</td> <td colspan="2" class="diff-lineno">Line 4:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB'''</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>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>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Botulinum neurotoxin serotype A (BoNTA) causes botulism<ref><ins style="color: red; font-weight: bold; text-decoration: none;">[http://ovidsp.tx.ovid.com/sp-2.3/ovidweb.cgi?&S=DOIGFPNAOODDJGOPNCELBHJLBPBGAA00&Link+Set=S.sh.15.16.19.40%7c11%7csl_10 </ins>Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)<ins style="color: red; font-weight: bold; text-decoration: none;">]</ins></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>.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb Download the coordinates of Model 1 (Hab1.pdb, PDB format)]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb Download the coordinates of Model 1 (Hab1.pdb, PDB format)]</div></td></tr> </table>

Yuan-Ping Pang