Classification and Exploration of 3D Protein Domain Interactions Using Kbdock
Identifieur interne : 000125 ( Main/Exploration ); précédent : 000124; suivant : 000126Classification and Exploration of 3D Protein Domain Interactions Using Kbdock
Auteurs : Anisah Ghoorah [France] ; Marie-Dominique Devignes [France] ; Malika Smaïl-Tabbone [France] ; David Ritchie [France]Source :
English descriptors
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Abstract
Comparing and classifying protein domain interactions according to theirthree-dimensional (3D) structures can help to understand protein structure-function and evolutionary relationships. Additionally, structural knowledge ofexisting domain–domain interactions can provide a useful way to findstructural templates with which to model the 3D structures of unsolvedprotein complexes. Here we present a straightforward guide to using the“Kbdock” protein domain structure database and its associated web site forexploring and comparing protein domain–domain interactions (DDIs) anddomain–peptide interactions (DPIs) at the Pfam domain family level. We alsobriefly explain how the Kbdock web site works, and we provide some notesand suggestions which should help to avoid some common pitfalls whenworking with 3D protein domain structures.
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DOI: 10.1007/978-1-4939-3572-7
Affiliations:
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Le document en format XML
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CS 25233 - 54052 Nancy cedex</addrLine><country key="FR"></country></address><ref type="url">http://www.univ-lorraine.fr/</ref></desc></org></tutelle><tutelle name="UMR7503" active="#struct-441569" type="indirect"><org type="institution" xml:id="struct-441569" status="VALID"><idno type="ISNI">0000000122597504</idno><idno type="IdRef">02636817X</idno><orgName>Centre National de la Recherche Scientifique</orgName><orgName type="acronym">CNRS</orgName><date type="start">1939-10-19</date><desc><address><country key="FR"></country></address><ref type="url">http://www.cnrs.fr/</ref></desc></org></tutelle></tutelles></hal:affiliation><country>France</country><placeName><settlement type="city">Nancy</settlement><settlement type="city">Metz</settlement><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region></placeName><orgName type="university">Université de Lorraine</orgName></affiliation></author><author><name sortKey="Ritchie, David" sort="Ritchie, David" uniqKey="Ritchie D" first="David" last="Ritchie">David Ritchie</name><affiliation wicri:level="1"><hal:affiliation type="researchteam" xml:id="struct-420402" status="VALID"><idno type="RNSR">201521171B</idno><orgName>Computational Algorithms for Protein Structures and Interactions</orgName><orgName type="acronym">CAPSID</orgName><desc><address><country key="FR"></country></address><ref type="url">http://www.inria.fr/equipes/capsid</ref></desc><listRelation><relation active="#struct-129671" type="direct"></relation><relation active="#struct-300009" type="indirect"></relation><relation active="#struct-423090" type="direct"></relation><relation active="#struct-206040" type="indirect"></relation><relation active="#struct-413289" type="indirect"></relation><relation name="UMR7503" active="#struct-441569" type="indirect"></relation></listRelation><tutelles><tutelle active="#struct-129671" type="direct"><org type="laboratory" xml:id="struct-129671" status="VALID"><idno type="RNSR">198618246Y</idno><orgName>INRIA Nancy - Grand Est</orgName><desc><address><addrLine>615 rue du Jardin Botanique 54600 Villers-lès-Nancy</addrLine><country key="FR"></country></address><ref type="url">http://www.inria.fr/nancy</ref></desc><listRelation><relation active="#struct-300009" type="direct"></relation></listRelation></org></tutelle><tutelle active="#struct-300009" type="indirect"><org type="institution" xml:id="struct-300009" status="VALID"><orgName>Institut National de Recherche en Informatique et en Automatique</orgName><orgName type="acronym">Inria</orgName><desc><address><addrLine>Domaine de VoluceauRocquencourt - BP 10578153 Le Chesnay Cedex</addrLine><country key="FR"></country></address><ref type="url">http://www.inria.fr/en/</ref></desc></org></tutelle><tutelle active="#struct-423090" type="direct"><org type="department" xml:id="struct-423090" status="VALID"><orgName>Department of Complex Systems, Artificial Intelligence & Robotics</orgName><orgName type="acronym">LORIA - AIS</orgName><desc><address><country key="FR"></country></address><ref type="url">http://www.loria.fr/la-recherche-en/departements/complex-system-and-artificial-intelligence</ref></desc><listRelation><relation active="#struct-206040" type="direct"></relation><relation active="#struct-300009" type="indirect"></relation><relation active="#struct-413289" type="indirect"></relation><relation name="UMR7503" active="#struct-441569" type="indirect"></relation></listRelation></org></tutelle><tutelle active="#struct-206040" type="indirect"><org type="laboratory" xml:id="struct-206040" status="VALID"><idno type="IdRef">067077927</idno><idno type="RNSR">198912571S</idno><idno type="IdUnivLorraine">[UL]RSI--</idno><orgName>Laboratoire Lorrain de Recherche en Informatique et ses Applications</orgName><orgName type="acronym">LORIA</orgName><date type="start">2012-01-01</date><desc><address><addrLine>Campus Scientifique BP 239 54506 Vandoeuvre-lès-Nancy Cedex</addrLine><country key="FR"></country></address><ref type="url">http://www.loria.fr</ref></desc><listRelation><relation active="#struct-300009" type="direct"></relation><relation active="#struct-413289" type="direct"></relation><relation name="UMR7503" active="#struct-441569" type="direct"></relation></listRelation></org></tutelle><tutelle active="#struct-413289" type="indirect"><org type="institution" xml:id="struct-413289" status="VALID"><idno type="IdRef">157040569</idno><idno type="IdUnivLorraine">[UL]100--</idno><orgName>Université de Lorraine</orgName><orgName type="acronym">UL</orgName><date type="start">2012-01-01</date><desc><address><addrLine>34 cours Léopold - CS 25233 - 54052 Nancy cedex</addrLine><country key="FR"></country></address><ref type="url">http://www.univ-lorraine.fr/</ref></desc></org></tutelle><tutelle name="UMR7503" active="#struct-441569" type="indirect"><org type="institution" xml:id="struct-441569" status="VALID"><idno type="ISNI">0000000122597504</idno><idno type="IdRef">02636817X</idno><orgName>Centre National de la Recherche Scientifique</orgName><orgName type="acronym">CNRS</orgName><date type="start">1939-10-19</date><desc><address><country key="FR"></country></address><ref type="url">http://www.cnrs.fr/</ref></desc></org></tutelle></tutelles></hal:affiliation><country>France</country><placeName><settlement type="city">Nancy</settlement><settlement type="city">Metz</settlement><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region></placeName><orgName type="university">Université de Lorraine</orgName></affiliation></author></analytic><idno type="DOI">10.1007/978-1-4939-3572-7</idno></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="mix" xml:lang="en"><term>Domain–domain interactions</term><term>Protein domain family</term><term>Protein domains</term><term>Structural biology</term><term>Structural homology</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Comparing and classifying protein domain interactions according to theirthree-dimensional (3D) structures can help to understand protein structure-function and evolutionary relationships. Additionally, structural knowledge ofexisting domain–domain interactions can provide a useful way to findstructural templates with which to model the 3D structures of unsolvedprotein complexes. Here we present a straightforward guide to using the“Kbdock” protein domain structure database and its associated web site forexploring and comparing protein domain–domain interactions (DDIs) anddomain–peptide interactions (DPIs) at the Pfam domain family level. We alsobriefly explain how the Kbdock web site works, and we provide some notesand suggestions which should help to avoid some common pitfalls whenworking with 3D protein domain structures.</div></front></TEI><affiliations><list><country><li>France</li></country><region><li>Grand Est</li><li>Lorraine (région)</li></region><settlement><li>Metz</li><li>Nancy</li></settlement><orgName><li>Université de Lorraine</li></orgName></list><tree><country name="France"><noRegion><name sortKey="Ghoorah, Anisah" sort="Ghoorah, Anisah" uniqKey="Ghoorah A" first="Anisah" last="Ghoorah">Anisah Ghoorah</name></noRegion><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" sort="Ritchie, David" uniqKey="Ritchie D" first="David" last="Ritchie">David 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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