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GRID‐MD—A tool for massive simulation of protein channels
Author(s) -
Carrillo Oliver,
Orozco Modesto
Publication year - 2008
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21592
Subject(s) - grid , molecular dynamics , millisecond , computer science , biological system , statistical physics , physics , biology , mathematics , geometry , astronomy , quantum mechanics
We present here a fast method for the exploration of channels in proteins based on molecular dynamics simulations of probe particles in a discrete grid space defined by an ensemble of protein conformations obtained either experimentally or by out‐of‐the‐grid atomistic molecular dynamics simulations. The method is able to provide millisecond‐long trajectories with a small computational effort, requires no human intervention in defining possible exit pathways and can detect both major and minor channels, giving a correct balance to the relative flux between them. The Grid‐Molecular‐Dynamics approach is then a suitable method for massive exploration of channels in proteins, even of those with unknown functional annotation. Proteins 2008. © 2007 Wiley‐Liss, Inc.