Intersurf: dynamic interface between proteins

Nicolas Ray; Xavier Cavin; Jean-Claude Paul; Bernard Maigret

inria-00105634, version 1

Intersurf: dynamic interface between proteins

Nicolas Ray^a^, 1, Xavier Cavin ()^a^, 1, Jean-Claude Paul ², Bernard Maigret^b^, 3, 4

Journal of Molecular Graphics and Modelling 23, 4 (2005) 347-354

Abstract: Protein docking is a fundamental biological process that links two proteins. This link is typically defined by an interaction between two large zones of the protein boundaries. Visualizing such an interface is useful to understand the process thanks to 3D protein structures, to estimate the quality of docking simulation results, and to classify interactions in order to predict docking affinity between classes of interacting zones. Since the interface may be defined by a surface that separates the two proteins, it is possible to create a map of interaction that allows comparisons to be performed in 2D. This paper presents a very fast algorithm that extracts an interface surface and creates a valid and low-distorted interaction map. Another benefit of our approach is that a pre-computed part of the algorithm enables the surface to be updated in real-time while residues are moved.

a – INRIA
b – UHP, NANCY
1: ISA (INRIA Lorraine - LORIA)
INRIA – CNRS : UMR7503 – Université Henri Poincaré - Nancy I – Université Nancy II – Institut National Polytechnique de Lorraine (INPL)
2: Tsinghua University
Tsinghua University
3: Structure et Réactivité des Systèmes Moléculaires Complexes (SRSMC)
CNRS : UMR7565 – Université Henri Poincaré - Nancy I
4: Laboratoire de chimie théorique (LCT)
CNRS : UMR7616 – Université Pierre et Marie Curie [UPMC] - Paris VI

inria-00105634, version 1
http://hal.inria.fr/inria-00105634
oai:hal.inria.fr:inria-00105634
From: Nicolas Ray <>
Submitted on: Wednesday, 11 October 2006 16:46:22
Updated on: Friday, 17 November 2006 11:17:47

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DOI: 10.1016/j.jmgm.2004.11.004

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