Spatial clustering of protein binding sites for template based protein docking
Identifieur interne : 002800 ( Main/Exploration ); précédent : 002799; suivant : 002801Spatial clustering of protein binding sites for template based protein docking
Auteurs : Anisah W. Ghoorah [France] ; Marie-Dominique Devignes [France] ; Malika Smaïl-Tabbone [France] ; David W. Ritchie [France]Source :
- Bioinformatics : (Oxford. Print) [ 1367-4803 ] ; 2011.
Descripteurs français
- KwdFr :
- Pascal (Inist)
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Multiprotein Complexes.
- methods : Protein Interaction Mapping.
- Binding Sites, Databases, Protein, Humans, Models, Molecular, Protein Interaction Domains and Motifs.
- mix :
Abstract
Motivation: 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. 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. Availability: http://kbdock.loria.fr/ Contact: Dave.Ritchie@inria.fr Supplementary Information: Supplementary data are available at Bioinformatics online.
Url:
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream PascalFrancis, to step Corpus: 000136
- to stream PascalFrancis, to step Curation: 000878
- to stream PascalFrancis, to step Checkpoint: 000120
- to stream Main, to step Merge: 002844
- to stream PubMed, to step Corpus: 000094
- to stream PubMed, to step Curation: 000094
- to stream PubMed, to step Checkpoint: 000091
- to stream Ncbi, to step Merge: 000121
- to stream Ncbi, to step Curation: 000119
- to stream Ncbi, to step Checkpoint: 000119
- to stream Hal, to step Corpus: 004672
- to stream Hal, to step Curation: 004672
- to stream Hal, to step Checkpoint: 001C39
- to stream Main, to step Merge: 002585
- to stream Main, to step Curation: 002800
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en" level="a">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 wicri:level="3"><inist:fA14 i1="01"><s1>INRIA, Campus Scientifique, BP 239</s1>
<s2>54506 Vandoeuvre-lès-Nancy</s2>
<s3>FRA</s3>
<sZ>1 aut.</sZ>
<sZ>4 aut.</sZ>
</inist:fA14>
<country>France</country>
<placeName><region type="region" nuts="2">Grand Est</region>
<region type="old region" nuts="2">Lorraine (région)</region>
<settlement type="city">Vandœuvre-lès-Nancy</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Devignes, Marie Dominique" sort="Devignes, Marie Dominique" uniqKey="Devignes M" first="Marie-Dominique" last="Devignes">Marie-Dominique Devignes</name>
<affiliation wicri:level="3"><inist:fA14 i1="02"><s1>CNRS, Campus Scientifique, BP 239</s1>
<s2>54506 Vandoeuvre-lès-Nancy</s2>
<s3>FRA</s3>
<sZ>2 aut.</sZ>
</inist:fA14>
<country>France</country>
<placeName><region type="region" nuts="2">Grand Est</region>
<region type="old region" nuts="2">Lorraine (région)</region>
<settlement type="city">Vandœuvre-lès-Nancy</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Smail Tabbone, Malika" sort="Smail Tabbone, Malika" uniqKey="Smail Tabbone M" first="Malika" last="Smaïl-Tabbone">Malika Smaïl-Tabbone</name>
<affiliation wicri:level="4"><inist:fA14 i1="03"><s1>Nancy Université, Orpailleur Team, LORIA, Campus Scientifique, BP 239</s1>
<s2>54506 Vandoeuvre-lès-Nancy</s2>
<s3>FRA</s3>
<sZ>3 aut.</sZ>
</inist:fA14>
<country>France</country>
<placeName><region type="region" nuts="2">Grand Est</region>
<region type="old region" nuts="2">Lorraine (région)</region>
<settlement type="city">Vandœuvre-lès-Nancy</settlement>
</placeName>
<orgName type="university">Nancy-Université</orgName>
</affiliation>
</author>
<author><name sortKey="Ritchie, David W" sort="Ritchie, David W" uniqKey="Ritchie D" first="David W." last="Ritchie">David W. Ritchie</name>
<affiliation wicri:level="3"><inist:fA14 i1="01"><s1>INRIA, Campus Scientifique, BP 239</s1>
<s2>54506 Vandoeuvre-lès-Nancy</s2>
<s3>FRA</s3>
<sZ>1 aut.</sZ>
<sZ>4 aut.</sZ>
</inist:fA14>
<country>France</country>
<placeName><region type="region" nuts="2">Grand Est</region>
<region type="old region" nuts="2">Lorraine (région)</region>
<settlement type="city">Vandœuvre-lès-Nancy</settlement>
</placeName>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">INIST</idno>
<idno type="inist">11-0455632</idno>
<date when="2011">2011</date>
<idno type="stanalyst">PASCAL 11-0455632 INIST</idno>
<idno type="RBID">Pascal:11-0455632</idno>
<idno type="wicri:Area/PascalFrancis/Corpus">000136</idno>
<idno type="wicri:Area/PascalFrancis/Curation">000878</idno>
<idno type="wicri:Area/PascalFrancis/Checkpoint">000120</idno>
<idno type="wicri:explorRef" wicri:stream="PascalFrancis" wicri:step="Checkpoint">000120</idno>
<idno type="wicri:doubleKey">1367-4803:2011:Ghoorah A:spatial:clustering:of</idno>
<idno type="wicri:Area/Main/Merge">002844</idno>
<idno type="wicri:source">PubMed</idno>
<idno type="RBID">pubmed: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>
<idno type="wicri:Area/PubMed/Curation">000094</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000094</idno>
<idno type="wicri:Area/PubMed/Checkpoint">000091</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000091</idno>
<idno type="wicri:Area/Ncbi/Merge">000121</idno>
<idno type="wicri:Area/Ncbi/Curation">000119</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">000119</idno>
<idno type="wicri:source">HAL</idno>
<idno type="RBID">Hal:inria-00617921</idno>
<idno type="url">https://hal.inria.fr/inria-00617921</idno>
<idno type="wicri:Area/Hal/Corpus">004672</idno>
<idno type="wicri:Area/Hal/Curation">004672</idno>
<idno type="wicri:Area/Hal/Checkpoint">001C39</idno>
<idno type="wicri:explorRef" wicri:stream="Hal" wicri:step="Checkpoint">001C39</idno>
<idno type="wicri:doubleKey">1367-4803:2011:Ghoorah A:spatial:clustering:of</idno>
<idno type="wicri:Area/Main/Merge">002585</idno>
<idno type="wicri:Area/Main/Curation">002800</idno>
<idno type="wicri:Area/Main/Exploration">002800</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a">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 wicri:level="3"><inist:fA14 i1="01"><s1>INRIA, Campus Scientifique, BP 239</s1>
<s2>54506 Vandoeuvre-lès-Nancy</s2>
<s3>FRA</s3>
<sZ>1 aut.</sZ>
<sZ>4 aut.</sZ>
</inist:fA14>
<country>France</country>
<placeName><region type="region" nuts="2">Grand Est</region>
<region type="old region" nuts="2">Lorraine (région)</region>
<settlement type="city">Vandœuvre-lès-Nancy</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Devignes, Marie Dominique" sort="Devignes, Marie Dominique" uniqKey="Devignes M" first="Marie-Dominique" last="Devignes">Marie-Dominique Devignes</name>
<affiliation wicri:level="3"><inist:fA14 i1="02"><s1>CNRS, Campus Scientifique, BP 239</s1>
<s2>54506 Vandoeuvre-lès-Nancy</s2>
<s3>FRA</s3>
<sZ>2 aut.</sZ>
</inist:fA14>
<country>France</country>
<placeName><region type="region" nuts="2">Grand Est</region>
<region type="old region" nuts="2">Lorraine (région)</region>
<settlement type="city">Vandœuvre-lès-Nancy</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Smail Tabbone, Malika" sort="Smail Tabbone, Malika" uniqKey="Smail Tabbone M" first="Malika" last="Smaïl-Tabbone">Malika Smaïl-Tabbone</name>
<affiliation wicri:level="4"><inist:fA14 i1="03"><s1>Nancy Université, Orpailleur Team, LORIA, Campus Scientifique, BP 239</s1>
<s2>54506 Vandoeuvre-lès-Nancy</s2>
<s3>FRA</s3>
<sZ>3 aut.</sZ>
</inist:fA14>
<country>France</country>
<placeName><region type="region" nuts="2">Grand Est</region>
<region type="old region" nuts="2">Lorraine (région)</region>
<settlement type="city">Vandœuvre-lès-Nancy</settlement>
</placeName>
<orgName type="university">Nancy-Université</orgName>
</affiliation>
</author>
<author><name sortKey="Ritchie, David W" sort="Ritchie, David W" uniqKey="Ritchie D" first="David W." last="Ritchie">David W. Ritchie</name>
<affiliation wicri:level="3"><inist:fA14 i1="01"><s1>INRIA, Campus Scientifique, BP 239</s1>
<s2>54506 Vandoeuvre-lès-Nancy</s2>
<s3>FRA</s3>
<sZ>1 aut.</sZ>
<sZ>4 aut.</sZ>
</inist:fA14>
<country>France</country>
<placeName><region type="region" nuts="2">Grand Est</region>
<region type="old region" nuts="2">Lorraine (région)</region>
<settlement type="city">Vandœuvre-lès-Nancy</settlement>
</placeName>
</affiliation>
</author>
</analytic>
<series><title level="j" type="main">Bioinformatics : (Oxford. Print)</title>
<title level="j" type="abbreviated">Bioinformatics : (Oxf., Print)</title>
<idno type="ISSN">1367-4803</idno>
<imprint><date when="2011">2011</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
<seriesStmt><title level="j" type="main">Bioinformatics : (Oxford. Print)</title>
<title level="j" type="abbreviated">Bioinformatics : (Oxf., Print)</title>
<idno type="ISSN">1367-4803</idno>
</seriesStmt>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Automatic classification</term>
<term>Binding Sites</term>
<term>Binding protein</term>
<term>Binding site</term>
<term>Cluster analysis</term>
<term>Databases, Protein</term>
<term>Docking</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="KwdFr" xml:lang="fr"><term>Bases de données de protéines</term>
<term>Cartographie d'interactions entre protéines ()</term>
<term>Complexes multiprotéiques ()</term>
<term>Humains</term>
<term>Modèles moléculaires</term>
<term>Motifs et domaines d'intéraction protéique</term>
<term>Sites de fixation</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>
<keywords scheme="Pascal" xml:lang="fr"><term>Analyse amas</term>
<term>Bases de données de protéines</term>
<term>Cartographie d'interactions entre protéines</term>
<term>Classification automatique</term>
<term>Complexes multiprotéiques</term>
<term>Humains</term>
<term>Modèles moléculaires</term>
<term>Motifs et domaines d'intéraction protéique</term>
<term>Protéine liaison</term>
<term>Site fixation</term>
<term>Arrimage</term>
<term>Sites de fixation</term>
</keywords>
<keywords scheme="mix" xml:lang="en"><term>Docking</term>
<term>Molecular modeling</term>
<term>Protein-protein interaction</term>
<term>Structural bioinformatics</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">Motivation: 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. 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. Availability: http://kbdock.loria.fr/ Contact: Dave.Ritchie@inria.fr Supplementary Information: Supplementary data are available at Bioinformatics online.</div>
</front>
</TEI>
<affiliations><list><country><li>France</li>
</country>
<region><li>Grand Est</li>
<li>Lorraine (région)</li>
</region>
<settlement><li>Vandœuvre-lès-Nancy</li>
</settlement>
<orgName><li>Nancy-Université</li>
</orgName>
</list>
<tree><country name="France"><region name="Grand Est"><name sortKey="Ghoorah, Anisah W" sort="Ghoorah, Anisah W" uniqKey="Ghoorah A" first="Anisah W." last="Ghoorah">Anisah W. Ghoorah</name>
</region>
<name sortKey="Devignes, Marie Dominique" sort="Devignes, Marie Dominique" uniqKey="Devignes M" first="Marie-Dominique" last="Devignes">Marie-Dominique Devignes</name>
<name sortKey="Ritchie, David W" sort="Ritchie, David W" uniqKey="Ritchie D" first="David W." last="Ritchie">David W. Ritchie</name>
<name sortKey="Smail Tabbone, Malika" sort="Smail Tabbone, Malika" uniqKey="Smail Tabbone M" first="Malika" last="Smaïl-Tabbone">Malika Smaïl-Tabbone</name>
</country>
</tree>
</affiliations>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Lorraine/explor/InforLorV4/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002800 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 002800 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Wicri/Lorraine |area= InforLorV4 |flux= Main |étape= Exploration |type= RBID |clé= Pascal:11-0455632 |texte= Spatial clustering of protein binding sites for template based protein docking }}
![]() | This area was generated with Dilib version V0.6.33. | ![]() |