Spatial clustering of protein binding sites for template based protein docking.
Identifieur interne : 000094 ( PubMed/Corpus ); précédent : 000093; suivant : 000095Spatial clustering of protein binding sites for template based protein docking.
Auteurs : Anisah W. Ghoorah ; Marie-Dominique Devignes ; Malika Smaïl-Tabbone ; David W. RitchieSource :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2011.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Multiprotein Complexes.
- methods : Protein Interaction Mapping.
- Binding Sites, Databases, Protein, Humans, Models, Molecular, Protein Interaction Domains and Motifs.
Abstract
In recent years, much structural information on protein domains and their pair-wise interactions has been made available in public databases. However, it is not yet clear how best to use this information to discover general rules or interaction patterns about structural protein-protein interactions. Improving our ability to detect and exploit structural interaction patterns will help to provide a better 3D picture of the known protein interactome, and will help to guide docking-based predictions of the 3D structures of unsolved protein complexes.
DOI: 10.1093/bioinformatics/btr493
PubMed: 21873637
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pubmed:21873637Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Spatial clustering of protein binding sites for template based protein docking.</title><author><name sortKey="Ghoorah, Anisah W" sort="Ghoorah, Anisah W" uniqKey="Ghoorah A" first="Anisah W" last="Ghoorah">Anisah W. Ghoorah</name><affiliation><nlm:affiliation>INRIA, LORIA, Campus Scientifique, BP 239, 54506 Vandoeuvre-lès-Nancy, France.</nlm:affiliation></affiliation></author><author><name sortKey="Devignes, Marie Dominique" sort="Devignes, Marie Dominique" uniqKey="Devignes M" first="Marie-Dominique" last="Devignes">Marie-Dominique Devignes</name></author><author><name sortKey="Smail Tabbone, Malika" sort="Smail Tabbone, Malika" uniqKey="Smail Tabbone M" first="Malika" last="Smaïl-Tabbone">Malika Smaïl-Tabbone</name></author><author><name sortKey="Ritchie, David W" sort="Ritchie, David W" uniqKey="Ritchie D" first="David W" last="Ritchie">David W. Ritchie</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2011">2011</date><idno type="doi">10.1093/bioinformatics/btr493</idno><idno type="RBID">pubmed:21873637</idno><idno type="pmid">21873637</idno><idno type="wicri:Area/PubMed/Corpus">000094</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000094</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Spatial clustering of protein binding sites for template based protein docking.</title><author><name sortKey="Ghoorah, Anisah W" sort="Ghoorah, Anisah W" uniqKey="Ghoorah A" first="Anisah W" last="Ghoorah">Anisah W. Ghoorah</name><affiliation><nlm:affiliation>INRIA, LORIA, Campus Scientifique, BP 239, 54506 Vandoeuvre-lès-Nancy, France.</nlm:affiliation></affiliation></author><author><name sortKey="Devignes, Marie Dominique" sort="Devignes, Marie Dominique" uniqKey="Devignes M" first="Marie-Dominique" last="Devignes">Marie-Dominique Devignes</name></author><author><name sortKey="Smail Tabbone, Malika" sort="Smail Tabbone, Malika" uniqKey="Smail Tabbone M" first="Malika" last="Smaïl-Tabbone">Malika Smaïl-Tabbone</name></author><author><name sortKey="Ritchie, David W" sort="Ritchie, David W" uniqKey="Ritchie D" first="David W" last="Ritchie">David W. Ritchie</name></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Binding Sites</term><term>Databases, Protein</term><term>Humans</term><term>Models, Molecular</term><term>Multiprotein Complexes (chemistry)</term><term>Protein Interaction Domains and Motifs</term><term>Protein Interaction Mapping (methods)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Multiprotein Complexes</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Protein Interaction Mapping</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Binding Sites</term><term>Databases, Protein</term><term>Humans</term><term>Models, Molecular</term><term>Protein Interaction Domains and Motifs</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">In recent years, much structural information on protein domains and their pair-wise interactions has been made available in public databases. However, it is not yet clear how best to use this information to discover general rules or interaction patterns about structural protein-protein interactions. Improving our ability to detect and exploit structural interaction patterns will help to provide a better 3D picture of the known protein interactome, and will help to guide docking-based predictions of the 3D structures of unsolved protein complexes.</div></front></TEI><pubmed><MedlineCitation Owner="NLM" Status="MEDLINE"><PMID Version="1">21873637</PMID><DateCreated><Year>2011</Year><Month>10</Month><Day>06</Day></DateCreated><DateCompleted><Year>2012</Year><Month>08</Month><Day>22</Day></DateCompleted><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN><JournalIssue CitedMedium="Internet"><Volume>27</Volume><Issue>20</Issue><PubDate><Year>2011</Year><Month>Oct</Month><Day>15</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>Spatial clustering of protein binding sites for template based protein docking.</ArticleTitle><Pagination><MedlinePgn>2820-7</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/btr493</ELocationID><Abstract><AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">In recent years, much structural information on protein domains and their pair-wise interactions has been made available in public databases. However, it is not yet clear how best to use this information to discover general rules or interaction patterns about structural protein-protein interactions. Improving our ability to detect and exploit structural interaction patterns will help to provide a better 3D picture of the known protein interactome, and will help to guide docking-based predictions of the 3D structures of unsolved protein complexes.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">This article presents KBDOCK, a 3D database approach for spatially clustering protein binding sites and for performing template-based (knowledge-based) protein docking. KBDOCK combines residue contact information from the 3DID database with the Pfam protein domain family classification together with coordinate data from the Protein Data Bank. This allows the 3D configurations of all known hetero domain-domain interactions to be superposed and clustered for each Pfam family. We find that most Pfam domain families have up to four hetero binding sites, and over 60% of all domain families have just one hetero binding site. The utility of this approach for template-based docking is demonstrated using 73 complexes from the Protein Docking Benchmark. Overall, up to 45 out of 73 complexes may be modelled by direct homology to existing domain interfaces, and key binding site information is found for 24 of the 28 remaining complexes. These results show that KBDOCK can often provide useful information for predicting the structures of unknown protein complexes.</AbstractText><AbstractText Label="AVAILABILITY" NlmCategory="BACKGROUND">http://kbdock.loria.fr/</AbstractText><AbstractText Label="CONTACT" NlmCategory="BACKGROUND">Dave.Ritchie@inria.fr</AbstractText><AbstractText Label="SUPPLEMENTARY INFORMATION" NlmCategory="BACKGROUND">Supplementary data are available at Bioinformatics online.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ghoorah</LastName><ForeName>Anisah W</ForeName><Initials>AW</Initials><AffiliationInfo><Affiliation>INRIA, LORIA, Campus Scientifique, BP 239, 54506 Vandoeuvre-lès-Nancy, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Devignes</LastName><ForeName>Marie-Dominique</ForeName><Initials>MD</Initials></Author><Author ValidYN="Y"><LastName>Smaïl-Tabbone</LastName><ForeName>Malika</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Ritchie</LastName><ForeName>David W</ForeName><Initials>DW</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><ArticleDate DateType="Electronic"><Year>2011</Year><Month>08</Month><Day>27</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Bioinformatics</MedlineTA><NlmUniqueID>9808944</NlmUniqueID><ISSNLinking>1367-4803</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D046912">Multiprotein Complexes</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName MajorTopicYN="N" UI="D001665">Binding Sites</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D030562">Databases, Protein</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D006801">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D008958">Models, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D046912">Multiprotein Complexes</DescriptorName><QualifierName MajorTopicYN="N" UI="Q000737">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="Y" UI="D054730">Protein Interaction Domains and Motifs</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D025941">Protein Interaction Mapping</DescriptorName><QualifierName MajorTopicYN="Y" UI="Q000379">methods</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="aheadofprint"><Year>2011</Year><Month>8</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2011</Year><Month>8</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2011</Year><Month>8</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2012</Year><Month>8</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pii">btr493</ArticleId><ArticleId IdType="doi">10.1093/bioinformatics/btr493</ArticleId><ArticleId IdType="pubmed">21873637</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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