Towards an interactive tool for the protein docking
Identifieur interne : 004E91 ( Hal/Curation ); précédent : 004E90; suivant : 004E92Towards an interactive tool for the protein docking
Auteurs : Matthieu Chavent [France]Source :
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Abstract
Protein-protein docking has become an extremely important challenge in biology, however, there remain two inherent difficulties: 1) most docking methods do not consider possible internal deformations of the proteins during their association; 2) it is not always easy to translate information from the literature or from experiments into constraints suitable for use in protein docking algorithms. Following these conclusions, we have developed an approach to improve existing docking programs. Firstly, through modelling the ERBIN PDZ / Smad3 MH2 complex, we have tested the utility of Molecular Dynamics with Explicit Solvent (MDSE) for elucidating the key residues in an interaction. We then extended this research by using several docking servers and the DMSE simulations to obtain a consensus result. Finally, we have explored the use of DMSE refinement on one of the targets from the CAPRI experiment and we have compared those results with those from short Monte-Carlo simulations. Another aspect of this thesis concerns the development of a novel molecular surface visualisation tool. This program, named MetaMol, allows the visualisation of a new type of molecular surface: the Molecular Skin Surface. Distributing the surface calculation between a computer's central processing unit (CPU) and its graphics card (GPU) allows deformations of the molecular surface to be calculated and visualised in real time.
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Université Henri Poincaré - Nancy I, 2009. Français</idno><idno type="halRef">Autre. Université Henri Poincaré - Nancy I, 2009. Français</idno></publicationStmt><seriesStmt><idno type="stamp" n="CNRS">CNRS - Centre national de la recherche scientifique</idno><idno type="stamp" n="INRIA">INRIA - Institut National de Recherche en Informatique et en Automatique</idno><idno type="stamp" n="INPL">Institut National Polytechnique de Lorraine</idno><idno type="stamp" n="LORIA2">Publications du LORIA</idno><idno type="stamp" n="INRIA-NANCY-GRAND-EST">INRIA Nancy - Grand Est</idno><idno type="stamp" n="LORIA-ACGI" p="LORIA">Algorithmique, calcul, image et géométrie</idno><idno type="stamp" n="LORIA">LORIA - Laboratoire Lorrain de Recherche en Informatique et ses Applications</idno><idno type="stamp" n="LORIA-TALC" p="LORIA">Traitement automatique des langues et des connaissances</idno><idno type="stamp" n="INRIA2">INRIA 2</idno><idno type="stamp" n="INRIA-LORRAINE">INRIA Nancy - Grand Est</idno><idno type="stamp" n="LABO-LORIA-SET" p="LORIA">LABO-LORIA-SET</idno><idno type="stamp" n="UNIV-LORRAINE">Université de Lorraine</idno></seriesStmt><notesStmt></notesStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Towards an interactive tool for the protein docking</title><title xml:lang="fr">Vers une nouvelle stratégie pour l'assemblage interactif de macromolécules</title><author role="aut"><persName><forename type="first">Matthieu</forename><surname>Chavent</surname></persName><idno type="halAuthorId">367427</idno><affiliation ref="#struct-2358"></affiliation><affiliation ref="#struct-3174"></affiliation></author></analytic><monogr><imprint><date type="dateDefended">2009-01-30</date></imprint><authority type="institution">Université Henri Poincaré - Nancy I</authority><authority type="school">Chimie et Sciences du Vivant</authority><authority type="supervisor">Bernard Maigret(Bernard.Maigret@loria.fr)</authority><authority type="jury">Gilbert DELEAGE (rapporteur)</authority><authority type="jury">Joel JANIN (rapporteur)</authority><authority type="jury">Jean-Paul BORG (examinateur)</authority><authority type="jury">Daniel CANET (examinateur)</authority><authority type="jury">Stephane REDON (examinateur)</authority><authority type="jury">Dave RITCHIE (examinateur)</authority><authority type="jury">Bernard MAIGRET (directeur)</authority><authority type="jury">Bruno LEVY (co-directeur)</authority></monogr></biblStruct></sourceDesc><profileDesc><langUsage><language ident="fr">French</language></langUsage><textClass><keywords scheme="author"><term xml:lang="fr">Docking</term><term xml:lang="fr">Interactions électrostatiques</term><term xml:lang="fr">Domaine PDZ d'ERBIN</term><term xml:lang="fr">Domaine MH2 de Smad3</term><term xml:lang="fr">GPU</term><term xml:lang="fr">Skin Surface Moléculaire</term><term xml:lang="fr">Déformations de surface</term><term xml:lang="fr">MetaMol</term></keywords><classCode scheme="halDomain" n="chim.othe">Chemical Sciences/Other</classCode><classCode scheme="halTypology" n="THESE">Theses</classCode></textClass><abstract xml:lang="en">Protein-protein docking has become an extremely important challenge in biology, however, there remain two inherent difficulties: 1) most docking methods do not consider possible internal deformations of the proteins during their association; 2) it is not always easy to translate information from the literature or from experiments into constraints suitable for use in protein docking algorithms. Following these conclusions, we have developed an approach to improve existing docking programs. Firstly, through modelling the ERBIN PDZ / Smad3 MH2 complex, we have tested the utility of Molecular Dynamics with Explicit Solvent (MDSE) for elucidating the key residues in an interaction. We then extended this research by using several docking servers and the DMSE simulations to obtain a consensus result. Finally, we have explored the use of DMSE refinement on one of the targets from the CAPRI experiment and we have compared those results with those from short Monte-Carlo simulations. Another aspect of this thesis concerns the development of a novel molecular surface visualisation tool. This program, named MetaMol, allows the visualisation of a new type of molecular surface: the Molecular Skin Surface. Distributing the surface calculation between a computer's central processing unit (CPU) and its graphics card (GPU) allows deformations of the molecular surface to be calculated and visualised in real time.</abstract><abstract xml:lang="fr">Même si le docking protéine-protéine devient un outil incontournable pour répondre aux problématiques biologiques actuelles, il reste cependant deux difficultés inhérentes aux méthodes actuelles: 1) la majorité de ces méthodes ne considère pas les possibles déformations internes des protéines durant leur association. 2) Il n'est pas toujours simple de traduire les informations issues de la littérature ou d'expérimentations en contraintes intégrables aux programmes de docking. Nous avons donc tenté de développer une approche permettant d'améliorer les programmes de docking existants. Pour cela nous nous sommes inspirés des méthodologies mises en place sur des cas concrets traités durant cette thèse. D'abord, à travers la création du complexe ERBIN PDZ/Smad3 MH2, nous avons pu tester l'utilité de la Dynamique Moléculaire en Solvant Explicite (DMSE) pour mettre en évidence des résidus importants pour l'interaction. Puis, nous avons étendu cette recherche en utilisant divers serveurs de docking puis la DMSE pour cibler un résultat consensus. Enfin, nous avons essayé le raffinage par DMSE sur une cible du challenge CAPRI et comparé les résultats avec des simulations courtes de Monte-Carlo. La dernière partie de cette thèse portait sur le développement d'un nouvel outil de visualisation de la surface moléculaire. Ce programme, nommé MetaMol, permet de visualiser un nouveau type de surface moléculaire: la Skin Surface Moléculaire. La distribution des calculs à la fois sur le processeur de l'ordinateur (CPU) et sur ceux de la carte graphique (GPU) entraine une diminution des temps de calcul autorisant la visualisation, en temps réel, des déformations de la surface moléculaire.</abstract></profileDesc></hal></record>Pour manipuler ce document sous Unix (Dilib)
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