Method of searching novel ligand compounds from three-dimensional structure database

A method of searching one or more ligand compound to a target biopolymer from a three-dimensional structure database, which comprises the steps of:

• (i) the first step of assigning hydrogen-bonding category numbers, information for calculating force-field energy, and information for generating conformations, to two or more trial compounds, in addition to atomic three-dimensional coordinates thereof;
• (ii) the second step of preparing physicochemical information about a ligand-binding region and one or more dummy atoms based on the three-dimensional atomic coordinates of the target biopolymer;
• (iii) the third step of estimating the most stable docking structure through structural optimization, wherein said step further comprises the steps of generating possible docking structures by docking a trial compound to the biopolymer while varying conformations of the trial compound, and evaluating interaction energy between the target biopolymer and the trial compound, based on the hydrogen-bonding category number, the information for calculating force-field energy, and the information for generating conformations assigned to the trial compound in addition to the three-dimensional coordinates according to the step (i) and based on the physicochemical information about the ligand-binding region prepared in the step (ii):
• (iv) the fourth step of deciding whether or not the trial compound should be adopted as a ligand candidate compound based on given criteria including the interaction energy values between the target biopolymer and the trial compound in the most stable docking structure found according to the step (iii);
• and
• (v) the fifth step of repeating the step (iii) and the step (iv) for all of the trial compounds.