GRID-MD-A tool for massive simulation of protein channels.
Title | GRID-MD-A tool for massive simulation of protein channels. |
Publication Type | Journal Article |
Year of Publication | 2008 |
Authors | Carrillo, Oliver, and Orozco Modesto |
Journal | Proteins |
Volume | 70 |
Pagination | 892-9 |
Date Published | 2008 Feb 15 |
ISSN | 1097-0134 |
Keywords | Algorithms, Binding Sites, Computer Simulation, Diffusion, Hydrogen Bonding, Ligands, Models, Molecular, Protein Conformation, Proteins, Software |
Abstract | 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. |
DOI | 10.1002/prot.21592 |