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.
Carrillo
Oliver
O
Molecular Modelling and Bioinformatics, Institut de Recerca Biomèdica, Parc Científic de Barcelona and Nacional Institut of Bioinformatics, Josep Samitier 1-5, Barcelona 08028, Spain.
Orozco
Modesto
M
D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D004058:Diffusion; D006860:Hydrogen Bonding; D008024:Ligands; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry; D012984:Software