Patent ID: 8145430

Claim:
A computer-implemented method for characterizing interaction of a proposed ligand with a specified receptor by accessing data from which the computer calculates a value representative of said interaction (VRI), said method comprising computer-scoring of hydrophobic interactions between one or more ligand atoms and one or more receptor atoms, said computer scoring comprising at least the following steps: a) the computer(s) receiving data from the database representative of atoms in the ligand docked with the receptor; b) the computer(s) acting on said data to identify groups of at least three covalently connected lipophilic ligand atoms that exhibit hydrophobic interaction with one or more lipophilic receptor atoms and scoring hydrophobic interactions of said ligand atoms with said receptor atoms; c) the computer(s) assigning a bonus for the presence of hydrophobic enclosure for each said group of at least three covalently connected lipophilic ligand atoms exhibiting hydrophobic interaction with receptor atoms on two sides of said group, and not for any group whose size is below three; and d) the computer(s) calculating the VRI including said bonus determined in step (c).