Patent ID: 7216041

Claim:
A method for selecting a chemical entity that associates with all or part of a binding pocket of a molecule or molecular complex, or a homologue of said binding pocket, with a deformation energy not greater than about 10 kcal/mole, wherein the structure coordinates of inosine monophosphate dehydrogenase (IMPDH) amino acids 68, 69, 93, 273, 274, 275, 276, 277, 303, 322, 324, 325, 326, 327, 328, 330, 331, 332, 333, 334, 337, 339, 340, 364, 413, 414, 415, 416, 420, 439, 440, 441, 442, 469, and 470 according to FIG. 1 characterize the binding pocket, and wherein the homologue of said binding pocket has a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å, comprising the steps of: a) determining structure coordinates of IMPDH amino acids 68, 69, 93, 273, 274, 275, 276, 277, 303, 322, 324, 325, 326, 327, 328, 330, 331, 332, 333, 334, 337, 339, 340, 364, 413, 414, 415, 416, 420, 439, 440, 441, 442, 469, and 470 according to FIG. 1 to characterize the binding pocket; b) employing computational means which utilize all or part of said structure coordinates and structure coordinates of the chemical entity, to dock the chemical entity with all or part of said binding pocket or homologue thereof; c) quantifying the deformation energy between the chemical entity and all or part of the binding pocket or homologue thereof; d) outputting said quantified deformation energy to a suitable output hardware; and e) selecting the chemical entity if said deformation energy is not greater than about 10 kcal/mole.