Exploring the conformational space of cyclic peptides by a stochastic search method.
Identifieur interne : 002392 ( PubMed/Corpus ); précédent : 002391; suivant : 002393Exploring the conformational space of cyclic peptides by a stochastic search method.
Auteurs : Anwar Rayan ; Hanoch Senderowitz ; Amiram GoldblumSource :
- Journal of molecular graphics & modelling [ 1093-3263 ] ; 2004.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Peptides, Cyclic.
- Algorithms, Data Interpretation, Statistical, Protein Conformation, Stochastic Processes.
Abstract
A stochastic search algorithm is applied in order to probe the conformations of cyclic peptides. The search is conducted in two stages. In the first stage, random conformations are generated and evaluated by a penalty function for ring closure ability, following a stepwise construction of each amino acid into the peptide by a random choice of one of its allowed conformations. The allowed conformational ranges of backbone dihedral angles for each amino acid have been extracted from a Data Bank of diverse proteins. Values of dihedral angles that do not contribute favorably to the scoring of ring closure are retained or discarded by a statistical test. Values are discarded up to a point from which all remaining combinations of angles are constructed, scored, sorted, and clustered. In the second stage, side chains have been added and fast optimization was applied to the set of diverse conformations in a "united atoms" approach, with the "Kollman forcefield" of Sybyl 6.8. This iterative stochastic elimination algorithm finds the global minimum and most of the best results, when compared to a full exhaustive search in appropriately sized problems. In larger problems, we compare the results to experimental structures. The root mean square deviation (RMSD) of our best results compared to crystal structures of cyclic peptides with sizes from 4 to 15 amino acids are mostly below 1.0 A up to 8 mers and under 2.0 A for larger cyclic peptides.
DOI: 10.1016/j.jmgm.2003.12.012
PubMed: 15099829
Links to Exploration step
pubmed:15099829Le document en format XML
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Bloom Center for Pharmacy, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem 91120, Israel. anvarr@md.huji.ac.il</nlm:affiliation></affiliation></author><author><name sortKey="Senderowitz, Hanoch" sort="Senderowitz, Hanoch" uniqKey="Senderowitz H" first="Hanoch" last="Senderowitz">Hanoch Senderowitz</name></author><author><name sortKey="Goldblum, Amiram" sort="Goldblum, Amiram" uniqKey="Goldblum A" first="Amiram" last="Goldblum">Amiram Goldblum</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2004">2004</date><idno type="RBID">pubmed:15099829</idno><idno type="pmid">15099829</idno><idno type="doi">10.1016/j.jmgm.2003.12.012</idno><idno type="wicri:Area/PubMed/Corpus">002392</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002392</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Exploring the conformational space of cyclic peptides by a stochastic search method.</title><author><name sortKey="Rayan, Anwar" sort="Rayan, Anwar" uniqKey="Rayan A" first="Anwar" last="Rayan">Anwar Rayan</name><affiliation><nlm:affiliation>Department of Medicinal Chemistry and Natural Products, David R. Bloom Center for Pharmacy, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem 91120, Israel. anvarr@md.huji.ac.il</nlm:affiliation></affiliation></author><author><name sortKey="Senderowitz, Hanoch" sort="Senderowitz, Hanoch" uniqKey="Senderowitz H" first="Hanoch" last="Senderowitz">Hanoch Senderowitz</name></author><author><name sortKey="Goldblum, Amiram" sort="Goldblum, Amiram" uniqKey="Goldblum A" first="Amiram" last="Goldblum">Amiram Goldblum</name></author></analytic><series><title level="j">Journal of molecular graphics & modelling</title><idno type="ISSN">1093-3263</idno><imprint><date when="2004" type="published">2004</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Data Interpretation, Statistical</term><term>Peptides, Cyclic (chemistry)</term><term>Protein Conformation</term><term>Stochastic Processes</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Peptides, Cyclic</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Data Interpretation, Statistical</term><term>Protein Conformation</term><term>Stochastic Processes</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">A stochastic search algorithm is applied in order to probe the conformations of cyclic peptides. The search is conducted in two stages. In the first stage, random conformations are generated and evaluated by a penalty function for ring closure ability, following a stepwise construction of each amino acid into the peptide by a random choice of one of its allowed conformations. The allowed conformational ranges of backbone dihedral angles for each amino acid have been extracted from a Data Bank of diverse proteins. Values of dihedral angles that do not contribute favorably to the scoring of ring closure are retained or discarded by a statistical test. Values are discarded up to a point from which all remaining combinations of angles are constructed, scored, sorted, and clustered. In the second stage, side chains have been added and fast optimization was applied to the set of diverse conformations in a "united atoms" approach, with the "Kollman forcefield" of Sybyl 6.8. This iterative stochastic elimination algorithm finds the global minimum and most of the best results, when compared to a full exhaustive search in appropriately sized problems. In larger problems, we compare the results to experimental structures. The root mean square deviation (RMSD) of our best results compared to crystal structures of cyclic peptides with sizes from 4 to 15 amino acids are mostly below 1.0 A up to 8 mers and under 2.0 A for larger cyclic peptides.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">15099829</PMID><DateCompleted><Year>2004</Year><Month>12</Month><Day>28</Day></DateCompleted><DateRevised><Year>2006</Year><Month>11</Month><Day>15</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">1093-3263</ISSN><JournalIssue CitedMedium="Print"><Volume>22</Volume><Issue>5</Issue><PubDate><Year>2004</Year><Month>May</Month></PubDate></JournalIssue><Title>Journal of molecular graphics & modelling</Title><ISOAbbreviation>J. Mol. Graph. Model.</ISOAbbreviation></Journal><ArticleTitle>Exploring the conformational space of cyclic peptides by a stochastic search method.</ArticleTitle><Pagination><MedlinePgn>319-33</MedlinePgn></Pagination><Abstract><AbstractText>A stochastic search algorithm is applied in order to probe the conformations of cyclic peptides. The search is conducted in two stages. In the first stage, random conformations are generated and evaluated by a penalty function for ring closure ability, following a stepwise construction of each amino acid into the peptide by a random choice of one of its allowed conformations. The allowed conformational ranges of backbone dihedral angles for each amino acid have been extracted from a Data Bank of diverse proteins. Values of dihedral angles that do not contribute favorably to the scoring of ring closure are retained or discarded by a statistical test. Values are discarded up to a point from which all remaining combinations of angles are constructed, scored, sorted, and clustered. In the second stage, side chains have been added and fast optimization was applied to the set of diverse conformations in a "united atoms" approach, with the "Kollman forcefield" of Sybyl 6.8. This iterative stochastic elimination algorithm finds the global minimum and most of the best results, when compared to a full exhaustive search in appropriately sized problems. In larger problems, we compare the results to experimental structures. The root mean square deviation (RMSD) of our best results compared to crystal structures of cyclic peptides with sizes from 4 to 15 amino acids are mostly below 1.0 A up to 8 mers and under 2.0 A for larger cyclic peptides.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Rayan</LastName><ForeName>Anwar</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Medicinal Chemistry and Natural Products, David R. Bloom Center for Pharmacy, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem 91120, Israel. anvarr@md.huji.ac.il</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Senderowitz</LastName><ForeName>Hanoch</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Goldblum</LastName><ForeName>Amiram</ForeName><Initials>A</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Mol Graph Model</MedlineTA><NlmUniqueID>9716237</NlmUniqueID><ISSNLinking>1093-3263</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010456">Peptides, Cyclic</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="N">Algorithms</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003627" MajorTopicYN="N">Data Interpretation, Statistical</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010456" MajorTopicYN="N">Peptides, Cyclic</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011487" MajorTopicYN="Y">Protein Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013269" MajorTopicYN="N">Stochastic Processes</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2004</Year><Month>4</Month><Day>22</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2004</Year><Month>12</Month><Day>29</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2004</Year><Month>4</Month><Day>22</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">15099829</ArticleId><ArticleId IdType="doi">10.1016/j.jmgm.2003.12.012</ArticleId><ArticleId IdType="pii">S1093-3263(03)00189-X</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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