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.