Protein-protein docking based on shape complementarity and Voronoi fingerprint

Thomas Bourquard; Jérôme Azé; Anne Poupon; David Ritchie

inria-00613186, version 1

Protein-protein docking based on shape complementarity and Voronoi fingerprint

Thomas Bourquard () ¹, Jérôme Azé ( Author to contact preferably ) ², Anne Poupon () ³, David Ritchie () ¹

Journées Ouvertes Biologie Informatique Mathématiques (2011) 9-16

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.

1: ORPAILLEUR (INRIA Lorraine - LORIA)
INRIA – CNRS : UMR7503 – Université Henri Poincaré - Nancy I – Université Nancy II – Institut National Polytechnique de Lorraine (INPL)
2: AMIB (INRIA Saclay - Ile de France)
INRIA – Polytechnique - X – CNRS : UMR8623 – Université Paris XI - Paris Sud
3: Physiologie de la reproduction et des comportements (PRC)
CNRS : UMR6175 – Institut national de la recherche agronomique (INRA) : UR0085 – Université François Rabelais - Tours

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From: David Ritchie <>
Submitted on: Wednesday, 3 August 2011 11:53:42
Updated on: Thursday, 4 August 2011 11:43:26

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%F inria-00613186, version 1
%0 Conference Proceedings
%U http://hal.inria.fr/inria-00613186
%2 INFO:INFO_BI;SDV:BIBS
%T Protein-protein docking based on shape complementarity and Voronoi fingerprint
%A Bourquard, Thomas
%A Azé, Jérôme
%A Poupon, Anne
%A Ritchie, David
%+ ORPAILLEUR - INRIA Lorraine - LORIA , AMIB - INRIA Saclay - Ile de France , Physiologie de la reproduction et des comportements - PRC
%X 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.
%2 La prédiction de la structure tri-dimensionnelle des complexes protéine-protéine est un enjeu majeur pour la bioinformatique. Nous avions montré dans des travaux précédents que grâce à la modélisation par un diagramme de Voronoï de la structure des protéines, et à l'utilisation d'algorithmes génétiques, il était possible d'optimiser des fonctions de score permettant de distinguer avec une bonne fiabilité les conformations natives des conformations non-natives. Nous montrons dans cet article que cette approche peut être sensiblement améliorée en combinant celle-ci avec des modèles en corps rigide générés par l'algorithme de docking Hex. Cette nouvelle approche, testée sur les cibles CAPRI des rounds 8 à 18, permet de classer dans les 10 meilleures, une conformation quasi-native pour 7 cibles sur les 9 disponibles.
%G French
%8 2011-07-28
%2 national
%B Journées Ouvertes Biologie Informatique Mathématiques
%2 Paris
%2 France
%8 2011-06-28
%8 2011-07-01
%E Emmanuel BARILLOT, Christine F ROIDEVAUX, Eduardo PC ROCHA
%I Institut Pasteur
%2 JOBIM 2011
%P 9-16
%K Protein-protein Docking; Evolutionary Algorithms; Hex; CAPRI
%2 9858

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