22. The method of claim 18 , wherein determining a profile further comprises assigning a score to at least one of the one or more patches based on a weight matrix, wherein the weight matrix describes a probability that a given position in a ligand structure is occupied by a given atom.
18. A method of screening a database of chemical compounds to identify leads for treating a disease, the method comprising: receiving, using a computer, ASCII structural descriptions of a set of input ligands and binding affinity data for the input ligands for a protein target known to be associated with the disease; determining, using the computer and from alignment data for the ASCII structural descriptions and from the binding affinity data, a profile comprising ASCII structural descriptions of one or more patches in the set of input ligands; storing the profile in one or more computer-readable media; and identifying one or more leads for treating the disease from a database comprising ASCII structural descriptions of a plurality of chemical compounds, the identifying comprising comparing the ASCII structural descriptions of the plurality of chemical compounds with the ASCII structural descriptions of the one or more patches, the ASCII structural descriptions of the identified one or more leads for treating the disease comprising the ASCII structural description of at least one of the one or more patches.