KBDOCK 2013: a spatial classification of 3D protein domain family interactions
Identifieur interne : 001401 ( Main/Exploration ); précédent : 001400; suivant : 001402KBDOCK 2013: a spatial classification of 3D protein domain family interactions
Auteurs : Anisah W. Ghoorah [France] ; Marie-Dominique Devignes [France] ; Malika Smaïl-Tabbone [France] ; David W. Ritchie [France]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2013.
Descripteurs français
- KwdFr :
- Alignement de séquences, Analyse de séquence de protéine, Bases de données de protéines, Cartes d'interactions protéiques, Cartographie d'interactions entre protéines, Internet, Modèles moléculaires, Motifs et domaines d'intéraction protéique, Protéines (), Simulation de docking moléculaire, Sites de fixation.
- MESH :
- Alignement de séquences, Analyse de séquence de protéine, Bases de données de protéines, Cartes d'interactions protéiques, Cartographie d'interactions entre protéines, Internet, Modèles moléculaires, Motifs et domaines d'intéraction protéique, Protéines, Simulation de docking moléculaire, Sites de fixation.
English descriptors
- KwdEn :
- MESH :
Abstract
Comparing, classifying and modelling protein structural interactions can enrich our understanding of many biomolecular processes. This contribution describes Kbdock (
Url:
DOI: 10.1093/nar/gkt1199
PubMed: 24271397
PubMed Central: 3964971
Affiliations:
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Le document en format XML
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Ghoorah</name><affiliation wicri:level="4"><nlm:aff id="gkt1199-AFF1">Université de Lorraine, LORIA, Campus Scientifique, BP 239, 54506 Villers-lès-Nancy, France,</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Université de Lorraine, LORIA, Campus Scientifique, BP 239, 54506 Villers-lès-Nancy</wicri:regionArea><placeName><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region><settlement type="city">Villers-lès-Nancy</settlement></placeName><orgName type="university">Université de Lorraine</orgName></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"><nlm:aff wicri:cut=" and" id="gkt1199-AFF1">CNRS, LORIA, Campus Scientifique, BP 239, 54506 Villers-lès-Nancy, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>CNRS, LORIA, Campus Scientifique, BP 239, 54506 Villers-lès-Nancy</wicri:regionArea><placeName><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region><settlement type="city">Villers-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"><nlm:aff id="gkt1199-AFF1">Université de Lorraine, LORIA, Campus Scientifique, BP 239, 54506 Villers-lès-Nancy, France,</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Université de Lorraine, LORIA, Campus Scientifique, BP 239, 54506 Villers-lès-Nancy</wicri:regionArea><placeName><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region><settlement type="city">Villers-lès-Nancy</settlement></placeName><orgName type="university">Université de Lorraine</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"><nlm:aff id="gkt1199-AFF1">INRIA Nancy Grand Est, LORIA, Campus Scientifique, BP 239, 54506 Villers-lès-Nancy, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INRIA Nancy Grand Est, LORIA, Campus Scientifique, BP 239, 54506 Villers-lès-Nancy</wicri:regionArea><placeName><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region><settlement type="city">Villers-lès-Nancy</settlement></placeName></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Binding Sites</term><term>Databases, Protein</term><term>Internet</term><term>Models, Molecular</term><term>Molecular Docking Simulation</term><term>Protein Interaction Domains and Motifs</term><term>Protein Interaction Mapping</term><term>Protein Interaction Maps</term><term>Proteins (classification)</term><term>Sequence Alignment</term><term>Sequence Analysis, Protein</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Alignement de séquences</term><term>Analyse de séquence de protéine</term><term>Bases de données de protéines</term><term>Cartes d'interactions protéiques</term><term>Cartographie d'interactions entre protéines</term><term>Internet</term><term>Modèles moléculaires</term><term>Motifs et domaines d'intéraction protéique</term><term>Protéines ()</term><term>Simulation de docking moléculaire</term><term>Sites de fixation</term></keywords><keywords scheme="MESH" type="chemical" qualifier="classification" xml:lang="en"><term>Proteins</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Binding Sites</term><term>Databases, Protein</term><term>Internet</term><term>Models, Molecular</term><term>Molecular Docking Simulation</term><term>Protein Interaction Domains and Motifs</term><term>Protein Interaction Mapping</term><term>Protein Interaction Maps</term><term>Sequence Alignment</term><term>Sequence Analysis, Protein</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term><term>Analyse de séquence de protéine</term><term>Bases de données de protéines</term><term>Cartes d'interactions protéiques</term><term>Cartographie d'interactions entre protéines</term><term>Internet</term><term>Modèles moléculaires</term><term>Motifs et domaines d'intéraction protéique</term><term>Protéines</term><term>Simulation de docking moléculaire</term><term>Sites de fixation</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Comparing, classifying and modelling protein structural interactions can enrich our understanding of many biomolecular processes. This contribution describes Kbdock (<ext-link ext-link-type="uri" xlink:href="http://kbdock.loria.fr/">http://kbdock.loria.fr/</ext-link>), a database system that combines the Pfam domain classification with coordinate data from the PDB to analyse and model 3D domain–domain interactions (DDIs). Kbdock can be queried using Pfam domain identifiers, protein sequences or 3D protein structures. For a given query domain or pair of domains, Kbdock retrieves and displays a non-redundant list of homologous DDIs or domain–peptide interactions in a common coordinate frame. Kbdock may also be used to search for and visualize interactions involving different, but structurally similar, Pfam families. Thus, structural DDI templates may be proposed even when there is little or no sequence similarity to the query domains.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Rose, Pw" uniqKey="Rose P">PW Rose</name></author><author><name sortKey="Bi, C" uniqKey="Bi C">C Bi</name></author><author><name sortKey="Bluhm, Wf" uniqKey="Bluhm W">WF Bluhm</name></author><author><name sortKey="Christie, Ch" uniqKey="Christie C">CH Christie</name></author><author><name sortKey="Dimitropoulos, D" uniqKey="Dimitropoulos D">D Dimitropoulos</name></author><author><name sortKey="Dutta, S" uniqKey="Dutta S">S Dutta</name></author><author><name sortKey="Green, Rk" uniqKey="Green R">RK Green</name></author><author><name sortKey="Goodsell, Ds" uniqKey="Goodsell D">DS Goodsell</name></author><author><name sortKey="Prlic, A" uniqKey="Prlic A">A Prlic</name></author><author><name sortKey="Quesada, M" uniqKey="Quesada M">M 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Tews</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tuncbag, N" uniqKey="Tuncbag N">N Tuncbag</name></author><author><name sortKey="Kar, G" uniqKey="Kar G">G Kar</name></author><author><name sortKey="Keskin, O" uniqKey="Keskin O">O Keskin</name></author><author><name sortKey="Gursoy, A" uniqKey="Gursoy A">A Gursoy</name></author><author><name sortKey="Nussinov, R" uniqKey="Nussinov R">R Nussinov</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kim, Wk" uniqKey="Kim W">WK Kim</name></author><author><name sortKey="Henschel, A" uniqKey="Henschel A">A Henschel</name></author><author><name sortKey="Winter, C" uniqKey="Winter C">C Winter</name></author><author><name sortKey="Schroeder, M" uniqKey="Schroeder M">M Schroeder</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Salwinski, L" uniqKey="Salwinski L">L Salwinski</name></author><author><name sortKey="Miller, Cs" uniqKey="Miller C">CS Miller</name></author><author><name sortKey="Smith, Aj" uniqKey="Smith A">AJ Smith</name></author><author><name sortKey="Pettit, Fk" uniqKey="Pettit F">FK Pettit</name></author><author><name sortKey="Bowie, Ju" uniqKey="Bowie J">JU Bowie</name></author><author><name sortKey="Eisenberg, D" uniqKey="Eisenberg D">D Eisenberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Alfarano, C" uniqKey="Alfarano C">C Alfarano</name></author><author><name sortKey="Andrade, Ce" uniqKey="Andrade C">CE Andrade</name></author><author><name sortKey="Anthony, K" uniqKey="Anthony K">K Anthony</name></author><author><name sortKey="Bahroos, N" uniqKey="Bahroos N">N Bahroos</name></author><author><name sortKey="Bajec, M" uniqKey="Bajec M">M Bajec</name></author><author><name sortKey="Bantoft, K" uniqKey="Bantoft K">K Bantoft</name></author><author><name sortKey="Betel, D" uniqKey="Betel D">D Betel</name></author><author><name sortKey="Bobechko, B" uniqKey="Bobechko B">B Bobechko</name></author><author><name sortKey="Boutilier, K" uniqKey="Boutilier K">K Boutilier</name></author><author><name sortKey="Burgess, E" uniqKey="Burgess E">E Burgess</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Petrey, D" uniqKey="Petrey D">D Petrey</name></author><author><name sortKey="Xiang, Z" uniqKey="Xiang Z">Z Xiang</name></author><author><name sortKey="Tang, Cl" uniqKey="Tang C">CL Tang</name></author><author><name sortKey="Xie, L" uniqKey="Xie L">L Xie</name></author><author><name sortKey="Gimpelev, M" uniqKey="Gimpelev M">M Gimpelev</name></author><author><name sortKey="Mitros, T" uniqKey="Mitros T">T Mitros</name></author><author><name sortKey="Soto, Cs" uniqKey="Soto C">CS Soto</name></author><author><name sortKey="Goldsmith Fischman, S" uniqKey="Goldsmith Fischman S">S Goldsmith-Fischman</name></author><author><name sortKey="Kernytsky, A" uniqKey="Kernytsky A">A Kernytsky</name></author><author><name sortKey="Schlessinger, A" uniqKey="Schlessinger A">A Schlessinger</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sali, A" uniqKey="Sali A">A Sali</name></author><author><name sortKey="Blundell, Tl" uniqKey="Blundell T">TL Blundell</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>France</li></country><region><li>Grand Est</li><li>Lorraine (région)</li></region><settlement><li>Villers-lès-Nancy</li></settlement><orgName><li>Université de Lorraine</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)
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