GRID-MD-A tool for massive simulation of protein channels.

TitleGRID-MD-A tool for massive simulation of protein channels.
Publication TypeJournal Article
Year of Publication2008
AuthorsCarrillo, Oliver, and Orozco Modesto
Date Published2008 Feb 15
KeywordsAlgorithms, Binding Sites, Computer Simulation, Diffusion, Hydrogen Bonding, Ligands, Models, Molecular, Protein Conformation, Proteins, Software

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.