title: pso@autodock: a fast flexible molecular docking program based on Swarm intelligence.
abstract: On the quest of novel therapeutics, molecular docking methods have proven to be valuable tools for screening large libraries of compounds determining the interactions of potential drugs with the target proteins. A widely used docking approach is the simulation of the docking process guided by a binding energy function. On the basis of the molecular docking program autodock, we present pso@autodock as a tool for fast flexible molecular docking. Our novel Particle Swarm Optimization (PSO) algorithms varCPSO and varCPSO-ls are suited for rapid docking of highly flexible ligands. Thus, a ligand with 23 rotatable bonds was successfully docked within as few as 100 000 computing steps (rmsd = 0.87 A), which corresponds to only 10% of the computing time demanded by autodock. In comparison to other docking techniques as gold 3.0, dock 6.0, flexx 2.2.0, autodock 3.05, and sodock, pso@autodock provides the smallest rmsd values for 12 in 37 protein-ligand complexes. The average rmsd value of 1.4 A is significantly lower then those obtained with the other docking programs, which are all above 2.0 A. Thus, pso@autodock is suggested as a highly efficient docking program in terms of speed and quality for flexible peptide-protein docking and virtual screening studies.
authors.affiliation: Faculty of Biosciences, Pharmacy and Psychology, Institute of Biochemistry, University of Leipzig, D-04103 Leipzig, Germany.
authors.forename: Vigneshwaran
authors.initials: V
authors.lastname: Namasivayam
authors.forename: Robert
authors.initials: R
authors.lastname: Günther
mesh_terms: D000465:Algorithms; D015195:Drug Design; D008024:Ligands; D010455:Peptides / Q000737:chemistry; D011506:Proteins / Q000737:chemistry; D012984:Software
chemical_list: D008024:Ligands; D010455:Peptides; D011506:Proteins