Patent ID: 6308145
Filing Date: 2001-10-23
Classification: G16B

Abstract:
A method which comprises:inputting three-dimensional coordinates for each atom of a biopolymer as well as atomic element, bond-type of covalent bonds and three-dimensional coordinates for each atom of a ligand;covering all possible docking structures between said biopolymer and said ligand while changing the conformation of said ligand by rotating torsion angles for each binding scheme; andoutputting information about three-dimensional coordinates for each atom of the ligand in one or more stable docking structures including the most stable docking structure relative to the biopolymer, the stability of said docking structures, as well as the binding modes and conformations of the ligand in said structures, wherein possible binding modes between the biopolymer and the ligand are covered by examining all combinations of correspondences between dummy atoms and heteroatoms in the ligand instead of changing relative positions and orientations between the two molecules, said dummy atoms being preset at the positions of heteroatoms that can be hydrogen-bonded with the hydrogen bonding groups in the biopolymer.