title: A hierarchical method for molecular docking using cloud computing.
abstract: Discovering small molecules that interact with protein targets will be a key part of future drug discovery efforts. Molecular docking of drug-like molecules is likely to be valuable in this field; however, the great number of such molecules makes the potential size of this task enormous. In this paper, a method to screen small molecular databases using cloud computing is proposed. This method is called the hierarchical method for molecular docking and can be completed in a relatively short period of time. In this method, the optimization of molecular docking is divided into two subproblems based on the different effects on the protein-ligand interaction energy. An adaptive genetic algorithm is developed to solve the optimization problem and a new docking program (FlexGAsDock) based on the hierarchical docking method has been developed. The implementation of docking on a cloud computing platform is then discussed. The docking results show that this method can be conveniently used for the efficient molecular design of drugs.
authors.affiliation: Department of Engineering Mechanics, State Key Laboratory of Structural Analysis for Industrial Equipment, Dalian University of Technology, Dalian 116023, PR China.
authors.forename: Ling
authors.initials: L
authors.lastname: Kang
authors.forename: Quan
authors.initials: Q
authors.lastname: Guo
authors.forename: Xicheng
authors.initials: X
authors.lastname: Wang
mesh_terms: D003201:Computers / Q000639:trends; D055808:Drug Discovery; D016247:Information Storage and Retrieval / Q000639:trends; D062105:Molecular Docking Simulation; D011485:Protein Binding; D054852:Small Molecule Libraries / Q000737:chemistry
chemical_list: D054852:Small Molecule Libraries