GRID‐MD—A tool for massive simulation of protein channels

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.