Vers une nouvelle stratégie pour l'assemblage interactif de macromolécules

Matthieu Chavent 1, 2
1 ORPAILLEUR - Knowledge representation, reasonning
INRIA Lorraine, LORIA - Laboratoire Lorrain de Recherche en Informatique et ses Applications
2 ALICE - Geometry and Lighting
INRIA Lorraine, LORIA - Laboratoire Lorrain de Recherche en Informatique et ses Applications
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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Matthieu Chavent. Vers une nouvelle stratégie pour l'assemblage interactif de macromolécules. Autre. Université Henri Poincaré - Nancy 1, 2009. Français. ⟨NNT : 2009NAN10111⟩. ⟨tel-01748503v2⟩

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