title: Bioinformatics based Ligand-Docking and in-silico screening.
abstract: We report a novel method, ChooseLD (CHOOse biological information Semi-Empirically on the Ligand Docking), which uses simulated annealing (SA) based on bioinformatics for protein-ligand flexible docking. The fingerprint alignment score (FPAScore) value is used to determine the docking conformation of the ligand. This method includes the matching of chemical descriptors such as fingerprints (FPs) and the root mean square deviation (rmsd) calculation of the coordinates of atoms of the chemical descriptors. Here, the FPAScore optimization for the translation and rotation of a rigid body is performed using the Metropolis Monte Carlo method. Our ChooseLD method will find wide application in the field of biochemistry and medicine to improve the search for new drugs targeting various proteins implicated in diseases.
authors.affiliation: School of Pharmacy, Kitasato University, Tokyo, Japan.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Takaya
authors.forename: Mayuko
authors.initials: M
authors.lastname: Takeda-Shitaka
authors.forename: Genki
authors.initials: G
authors.lastname: Terashi
authors.forename: Kazuhiko
authors.initials: K
authors.lastname: Kanou
authors.forename: Mitsuo
authors.initials: M
authors.lastname: Iwadate
authors.forename: Hideaki
authors.initials: H
authors.lastname: Umeyama
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D003198:Computer Simulation; D016172:DNA Fingerprinting; D004353:Drug Evaluation, Preclinical / Q000379:methods*; D008024:Ligands; D008957:Models, Genetic; D015233:Models, Statistical; D011485:Protein Binding
chemical_list: D008024:Ligands