1. A computer-implemented method for generating a database of pharmacophores, comprising the steps of: (a) defining a joint pharmacophore space comprising a plurality of pharmacophores, each of the plurality of pharmacophores comprising a geometric arrangement of at least three pharmacophoric features; (b) identifying subspaces within the joint pharmacophore space, each subspace having an associated subset of the pharmacophores with similar geometric arrangements; (c) assigning a biological activity property and a representative geometric arrangement for each subspace identified to correlate with a targeted biological activity; and (d) storing the joint pharmacophore space, subspaces, biological activity properties, and representative geometric arrangements.