Comparing atom-based with residue-based descriptors in predicting binding site similarity: do backbone atoms matter?
Identifieur interne : 001716 ( PubMed/Curation ); précédent : 001715; suivant : 001717Comparing atom-based with residue-based descriptors in predicting binding site similarity: do backbone atoms matter?
Auteurs : Noé Sturm [France] ; Didier Rognan [France] ; Ronald J. Quinn [Australie] ; Esther Kellenberger [France]Source :
- Future medicinal chemistry [ 1756-8927 ] ; 2016.
Abstract
We question the level of detail required in protein 3D-representation to detect site similarity which is relevant for polypharmacology prediction.
DOI: 10.4155/fmc-2016-0077
PubMed: 27629811
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Quinn</name><affiliation wicri:level="1"><nlm:affiliation>Eskitis Institute for Drug Discovery, Griffith University, Innovation Park, Don Young Road, Nathan, Brisbane, QLD 4111, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Eskitis Institute for Drug Discovery, Griffith University, Innovation Park, Don Young Road, Nathan, Brisbane, QLD 4111</wicri:regionArea></affiliation></author><author><name sortKey="Kellenberger, Esther" sort="Kellenberger, Esther" uniqKey="Kellenberger E" first="Esther" last="Kellenberger">Esther Kellenberger</name><affiliation wicri:level="1"><nlm:affiliation>UMR 7200 CNRS/Université de Strasbourg, MEDALIS Drug Discovery Center, 74 Route du Rhin, 67401, Illkirch, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>UMR 7200 CNRS/Université de Strasbourg, MEDALIS Drug Discovery Center, 74 Route du Rhin, 67401, Illkirch</wicri:regionArea></affiliation></author></analytic><series><title level="j">Future medicinal chemistry</title><idno type="eISSN">1756-8927</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We question the level of detail required in protein 3D-representation to detect site similarity which is relevant for polypharmacology prediction.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">27629811</PMID><DateCreated><Year>2016</Year><Month>09</Month><Day>30</Day></DateCreated><DateRevised><Year>2016</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1756-8927</ISSN><JournalIssue CitedMedium="Internet"><Volume>8</Volume><Issue>15</Issue><PubDate><Year>2016</Year><Month>Oct</Month></PubDate></JournalIssue><Title>Future medicinal chemistry</Title><ISOAbbreviation>Future Med Chem</ISOAbbreviation></Journal><ArticleTitle>Comparing atom-based with residue-based descriptors in predicting binding site similarity: do backbone atoms matter?</ArticleTitle><Pagination><MedlinePgn>1871-1885</MedlinePgn></Pagination><Abstract><AbstractText Label="AIM" NlmCategory="OBJECTIVE">We question the level of detail required in protein 3D-representation to detect site similarity which is relevant for polypharmacology prediction.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We modified the in-house program SiteAlign to replace generic pharmacophoric descriptors of cavity-lining amino acids by descriptors accounting for solvent exposure. Benchmarking the novel, atom-based, method (SiteAlign2) revealed no global improvement of performance. However, in the rare cases of no sequence or global structure similarities between the compared proteins, SiteAlign2 was more successful if backbone atoms are key determinants of ligand binding.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">SiteAlign suits the comparison of binding sites for close or distant homologs. SiteAlign2 provides a better insight into the physical model of site similarity between nonhomologs, but at the expense of an increased sensitivity to atomic coordinates.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Sturm</LastName><ForeName>Noé</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>UMR 7200 CNRS/Université de Strasbourg, MEDALIS Drug Discovery Center, 74 Route du Rhin, 67401, Illkirch, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Eskitis Institute for Drug Discovery, Griffith University, Innovation Park, Don Young Road, Nathan, Brisbane, QLD 4111, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rognan</LastName><ForeName>Didier</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>UMR 7200 CNRS/Université de Strasbourg, MEDALIS Drug Discovery Center, 74 Route du Rhin, 67401, Illkirch, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Quinn</LastName><ForeName>Ronald J</ForeName><Initials>RJ</Initials><AffiliationInfo><Affiliation>Eskitis Institute for Drug Discovery, Griffith University, Innovation Park, Don Young Road, Nathan, Brisbane, QLD 4111, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kellenberger</LastName><ForeName>Esther</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>UMR 7200 CNRS/Université de Strasbourg, MEDALIS Drug Discovery Center, 74 Route du Rhin, 67401, Illkirch, France.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>09</Month><Day>15</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Future Med Chem</MedlineTA><NlmUniqueID>101511162</NlmUniqueID><ISSNLinking>1756-8919</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">3D alignment</Keyword><Keyword MajorTopicYN="N">fingerprint</Keyword><Keyword MajorTopicYN="N">ligand–protein interaction</Keyword><Keyword MajorTopicYN="N">protein superimposition</Keyword><Keyword MajorTopicYN="N">scoring</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>9</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>9</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>9</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27629811</ArticleId><ArticleId IdType="doi">10.4155/fmc-2016-0077</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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