10. The method of claim 1 , wherein the set of input ligands are inhibitors of the target protein known to be associated with the disease.
1. A method of screening a database of molecules to identify leads for treating a disease, the method comprising: generating, using a computer, from aligned structural descriptions of a set of input ligands and from binding affinity data for the set of input ligands for a target protein known to be associated with the disease, a profile comprising ASCII structural descriptions of one or more patches in the set of input ligands; identifying, using the computer, a set of one or more leads for treating the disease from a database, the identifying based at least in part on the profile, wherein the database comprises ASCII structural descriptions of a plurality of molecules, the ASCII structural descriptions of the plurality of molecules comprising force field information for one or more atoms described in the ASCII structural descriptions of the plurality of molecules, the identifying comprising comparing the ASCII structural descriptions of the plurality of molecules with the ASCII structural descriptions of the one or more patches, the ASCII structural descriptions of the one or more leads for treating the disease comprising the ASCII structural description of at least one of the one or more patches; and storing the ASCII structural descriptions of the set of one or more leads for treating the disease in one or more computer-readable media.