Patent ID: 7716030

Claim:
A method of identifying potential ligands for protein targets comprising: (1) providing a set of models, wherein each model comprises three-dimensional structural information for a ligand or a ligand: protein complex, wherein each ligand comprises a plurality of atoms and a plurality of bonds, wherein each model is related to the other models of the set by 25% or more sequence homology for proteins, or by; a structural homology between the ligands of at least 4-6 atoms in common; and wherein the structural information is derived from physical observation and/or computational inference; (2) mapping spatial relationships between the models such that the models are superimposed with respect to the homologous structural feature; (3) identifying one or more pairs of matching bonds between ligands of the set, wherein the matching bonds comprise a bond of a first ligand (B1) and a bond of a second ligand (B2) that are superimposed in step (2) such that (i) an atom at each end of the bond (B1) is within 1.8 angstrom of an atom at each end of the bond (B2), (ii) the bond (B1) and the corresponding bond (B2) are of the same bond order, and (iii) the bond (B1) and the corresponding bond (B2) are related by an angle of 30° or less; (4) selecting a plurality of subsets of atoms and/or bonds from each ligand; wherein each subset comprises a bond and/or, an atom connected to the matching bond as identified in (3); (5) generating and displaying output ligands, each output ligand comprising atoms and/or bonds of a first subset as selected in (4) and atoms and/or bonds of a second subset as selected in (4), wherein the first subset and the second subset comprise atoms and/or bonds derived from opposite ends of a matching bond as selected in (4) wherein steps (1) through (5) are performed by a suitably programmed computer.