Protein-protein docking based on shape complementarity and Voronoi fingerprint
Identifieur interne : 002265 ( Main/Exploration ); précédent : 002264; suivant : 002266Protein-protein docking based on shape complementarity and Voronoi fingerprint
Auteurs : Thomas Bourquard [France] ; Jérôme Azé [France] ; Anne Poupon [France] ; David Ritchie [France]Source :
English descriptors
Abstract
Predicting the three-dimensional structures of protein-protein complexes is a major challenge for computational biology. Using a Voronoi tessellation model of protein structure, we showed previously that it was possible to use an evolutionary algorithm to train a scoring function to distinguish reliably between native and non-native docking conformations. Here, we show that this approach can be further improved by combining it with rigid body docking predictions generated by the Hex docking algorithm. This new approach is able to rank an acceptable or better conformation within the top 10 predictions for 7 out of the 9 targets available from rounds 8 to 18 of the CAPRI docking experiment.
Url:
Affiliations:
- France
- Centre-Val de Loire, Grand Est, Lorraine (région), Région Centre
- Nancy, Tours
- Centre Val de Loire Université, Institut national polytechnique de Lorraine, Université Nancy 2, Université de Lorraine, Université de Tours
Links toward previous steps (curation, corpus...)
- to stream Hal, to step Corpus: 003E15
- to stream Hal, to step Curation: 003E15
- to stream Hal, to step Checkpoint: 001D32
- to stream Main, to step Merge: 002310
- to stream Main, to step Curation: 002265
Le document en format XML
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type="acronym">INPL</orgName><date type="end">2011-12-31</date><desc><address><country key="FR"></country></address></desc></org></tutelle><tutelle active="#struct-2496" type="direct"><org type="laboratory" xml:id="struct-2496" status="OLD"><orgName>INRIA Lorraine</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/centre-de-recherche-inria/nancy-grand-est</ref></desc><listRelation><relation active="#struct-300009" type="direct"></relation></listRelation></org></tutelle></tutelles></hal:affiliation><country>France</country><placeName><settlement type="city">Nancy</settlement><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region></placeName><orgName type="university">Université Nancy 2</orgName><orgName type="institution" wicri:auto="newGroup">Université de Lorraine</orgName><placeName><settlement type="city">Nancy</settlement><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region></placeName><orgName type="university">Institut national polytechnique de Lorraine</orgName><orgName type="institution" wicri:auto="newGroup">Université de Lorraine</orgName></affiliation></author></analytic></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="mix" xml:lang="en"><term>CAPRI</term><term>Evolutionary Algorithms</term><term>Hex</term><term>Protein-protein Docking</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Predicting the three-dimensional structures of protein-protein complexes is a major challenge for computational biology. Using a Voronoi tessellation model of protein structure, we showed previously that it was possible to use an evolutionary algorithm to train a scoring function to distinguish reliably between native and non-native docking conformations. Here, we show that this approach can be further improved by combining it with rigid body docking predictions generated by the Hex docking algorithm. This new approach is able to rank an acceptable or better conformation within the top 10 predictions for 7 out of the 9 targets available from rounds 8 to 18 of the CAPRI docking experiment.</div></front></TEI><affiliations><list><country><li>France</li></country><region><li>Centre-Val de Loire</li><li>Grand Est</li><li>Lorraine (région)</li><li>Région Centre</li></region><settlement><li>Nancy</li><li>Tours</li></settlement><orgName><li>Centre Val de Loire Université</li><li>Institut national polytechnique de Lorraine</li><li>Université Nancy 2</li><li>Université de Lorraine</li><li>Université de Tours</li></orgName></list><tree><country name="France"><region name="Grand Est"><name sortKey="Bourquard, Thomas" sort="Bourquard, Thomas" uniqKey="Bourquard T" first="Thomas" last="Bourquard">Thomas Bourquard</name></region><name sortKey="Aze, Jerome" sort="Aze, Jerome" uniqKey="Aze J" first="Jérôme" last="Azé">Jérôme Azé</name><name sortKey="Poupon, Anne" sort="Poupon, Anne" uniqKey="Poupon A" first="Anne" last="Poupon">Anne Poupon</name><name sortKey="Ritchie, David" sort="Ritchie, David" uniqKey="Ritchie D" first="David" last="Ritchie">David Ritchie</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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