title: iMOLSDOCK: Induced-fit docking using mutually orthogonal Latin squares (MOLS).
abstract: We have earlier reported the MOLSDOCK technique to perform rigid receptor/flexible ligand docking. The method uses the MOLS method, developed in our laboratory. In this paper we report iMOLSDOCK, the 'flexible receptor' extension we have carried out to the algorithm MOLSDOCK. iMOLSDOCK uses mutually orthogonal Latin squares (MOLS) to sample the conformation and the docking pose of the ligand and also the flexible residues of the receptor protein. The method then uses a variant of the mean field technique to analyze the sample to arrive at the optimum. We have benchmarked and validated iMOLSDOCK with a dataset of 44 peptide-protein complexes with peptides. We have also compared iMOLSDOCK with other flexible receptor docking tools GOLD v5.2.1 and AutoDock Vina. The results obtained show that the method works better than these two algorithms, though it consumes more computer time.
authors.affiliation: Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai 600025, India.
authors.forename: D Sam
authors.initials: DS
authors.lastname: Paul
authors.affiliation: Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai 600025, India. Electronic address: n_gautham@hotmail.com.
authors.forename: N
authors.initials: N
authors.lastname: Gautham
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D006801:Humans; D006860:Hydrogen Bonding; D062105:Molecular Docking Simulation / Q000379:methods*; D009842:Oligopeptides / Q000737:chemistry; D011485:Protein Binding; D000072757:Protein Conformation, beta-Strand; D011956:Receptors, Cell Surface / Q000737:chemistry; D012984:Software; D013816:Thermodynamics
chemical_list: D009842:Oligopeptides; D011956:Receptors, Cell Surface
keywords: Docking tool; Induced-fit docking; MOLSDOCK; Molecular docking; Mutually orthogonal Latin squares; Peptide-protein docking; Receptor flexibility; Side-chain flexibility