Encoding molecular motions in voxels maps
Résumé
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.
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