Encoding molecular motions in voxel maps

Authors:
Juan Cortés;Sophie Barbe;Monique Erard;Thierry Siméon
Affiliations:
LAAS-CNRS, Toulouse, France and Université de Toulouse, UPS, INSA, INP, ISAE, Toulouse, France;LISBP, Toulouse, France and Université de Toulouse, UPS, INSA, INP, ISAE, Toulouse, France;IPBS, Toulouse, France and Université de Toulouse, UPS, INSA, INP, ISAE, Toulouse, France;LAAS-CNRS, Toulouse, France and Université de Toulouse, UPS, INSA, INP, ISAE, Toulouse, France
Venue:
ICRA'09 Proceedings of the 2009 IEEE international conference on Robotics and Automation
Year:
2009

Citing 6
Cited 1

Molecular Modeling and Simulation: An Interdisciplinary Guide

Molecular Modeling and Simulation: An Interdisciplinary Guide
A Motion Planning Approach to Flexible Ligand Binding

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A path planning approach for computing large-amplitude motions of flexible molecules

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Planning Algorithms

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Prediction and simulation of motion in pairs of transmembrane α-helices

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Encoding Molecular Motions in Voxel Maps

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

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Abstract

Understanding life at the atomic level requires the development of new methodologies, able to overcome the limitations of available experimental and computational techniques for the analysis of processes involving molecular motions. With this goal in mind, we develop new methods, combining robotic path planning algorithms and molecular modeling techniques, for computing large-amplitude motions. This paper builds on these new methods, and introduces voxel maps as a computational tool to encode and to represent such motions. Voxel maps can be used to represent relative motions of two molecules, as well as conformational changes in macromolecules. We investigate several applications and show results that illustrate the interest of such representation. In particular, voxel maps are used to display channels into proteins, to analyze protein-ligand specificity, and to represents protein loop and domain motions.