Patent Document ID: 20030167136
Application ID: 10213122
Patent Flag: 0

Claim One:
1. A method for determining if a candidate molecule is docked to a target molecule, the method comprising the steps of: a. determining a pseudo-energy function, E, between a target molecule and a candidate molecule for one or more of the possible positions P i of each atom, i, comprising the candidate molecule; b. determining a function for the partial derivatives of E with respect to P i for each atom i; c. determining an initial set of geometric parameters, Q j, describing the conformation of the candidate molecule; d. determining partial derivatives of P i with respect to one or more of the Q j ; e. determining the dot product of 25 &PartialD; E &PartialD; P i &CenterDot; &PartialD; P i &PartialD; Q j for one or more of the Q j ; f. summing each dot product determined in part e over the i atoms comprising the candidate molecule, thereby determining partial derivatives of E as a function of the geometric parameters comprising the set Q; g. calculating a new set of geometric parameters based on the partial derivatives of E as a function of the geometric parameters calculated in step f; h. calculating a pseudo-energy for the candidate molecule with a conformation described by the new set of geometric parameters; i. if the pseudo-energy is less than a threshold energy, identifying the candidate molecule as docked; j. if the pseudo-energy is not less than a threshold energy, repeating steps d through j until a criteria is satisfied.