title: 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 introduce the PELE web server, designed to make the whole process of running simulations easier and more practical by minimizing input file demand, providing user-friendly interface and producing abstract outputs (e.g. interactive graphs and tables). The web server has been implemented in C++ using Wt (http://www.webtoolkit.eu) and MySQL (http://www.mysql.com). The PELE web server, accessible at http://pele.bsc.es, is free and open to all users with no login requirement.
authors.affiliation: Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain. armin.madadkar@bsc.es
authors.forename: Armin
authors.initials: A
authors.lastname: Madadkar-Sobhani
authors.forename: Victor
authors.initials: V
authors.lastname: Guallar
mesh_terms: D000465:Algorithms; D001241:Aspirin / Q000737:chemistry; D020407:Internet; D008024:Ligands; D008958:Models, Molecular; D009010:Monte Carlo Method; D054467:Phospholipases A2 / Q000737:chemistry; D011487:Protein Conformation; D018160:Receptors, Cytoplasmic and Nuclear / Q000737:chemistry; D012984:Software
chemical_list: D008024:Ligands; D018160:Receptors, Cytoplasmic and Nuclear; D054467:Phospholipases A2; D001241:Aspirin