PELE web server: atomistic study of biomolecular systems at your fingertips.

ABSTRACT: PELE, Protein Energy Landscape Exploration, our novel technology based on protein structure prediction algorithms and a Monte Carlo sampling, is capable of modelling the all-atom protein-ligand dynamical interactions in an efficient and fast manner, with two orders of magnitude reduced computational cost when compared with traditional molecular dynamics techniques. PELE's heuristic approach generates trial moves based on protein and ligand perturbations followed by side chain sampling and global/local minimization. The collection of accepted steps forms a stochastic trajectory. Furthermore, several processors may be run in parallel towards a collective goal or defining several independent trajectories; the whole procedure has been parallelized using the Message Passing Interface. Here, we

SUBMITTER: Madadkar-Sobhani A 

PROVIDER: S-EPMC3692087 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature