title: FIPSDock: a new molecular docking technique driven by fully informed swarm optimization algorithm.
abstract: The accurate prediction of protein-ligand binding is of great importance for rational drug design. We present herein a novel docking algorithm called as FIPSDock, which implements a variant of the Fully Informed Particle Swarm (FIPS) optimization method and adopts the newly developed energy function of AutoDock 4.20 suite for solving flexible protein-ligand docking problems. The search ability and docking accuracy of FIPSDock were first evaluated by multiple cognate docking experiments. In a benchmarking test for 77 protein/ligand complex structures derived from GOLD benchmark set, FIPSDock has obtained a successful predicting rate of 93.5% and outperformed a few docking programs including particle swarm optimization (PSO)@AutoDock, SODOCK, AutoDock, DOCK, Glide, GOLD, FlexX, Surflex, and MolDock. More importantly, FIPSDock was evaluated against PSO@AutoDock, SODOCK, and AutoDock 4.20 suite by cross-docking experiments of 74 protein-ligand complexes among eight protein targets (CDK2, ESR1, F2, MAPK14, MMP8, MMP13, PDE4B, and PDE5A) derived from Sutherland-crossdock-set. Remarkably, FIPSDock is superior to PSO@AutoDock, SODOCK, and AutoDock in seven out of eight cross-docking experiments. The results reveal that FIPS algorithm might be more suitable than the conventional genetic algorithm-based algorithms in dealing with highly flexible docking problems.
authors.affiliation: School of Software, Dalian University of Technology, Dalian 116023, People's Republic of China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Liu
authors.forename: Lei
authors.initials: L
authors.lastname: Zhao
authors.forename: Wentao
authors.initials: W
authors.lastname: Li
authors.forename: Dongyu
authors.initials: D
authors.lastname: Zhao
authors.forename: Miao
authors.initials: M
authors.lastname: Song
authors.forename: Yongliang
authors.initials: Y
authors.lastname: Yang
mesh_terms: D000465:Algorithms; D008024:Ligands; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry*
chemical_list: D008024:Ligands; D011506:Proteins