Molecular transformations as a way of finding and exploiting consistent local QSAR.

The idea of a "transformation", making a small change to a chemical structure, for instance removing or replacing a substituent, is familiar to chemists. We suggest two ways of representing a transformation in silico, as a substructure descriptor difference vector, and as the set of atoms remaining once a maximum common substructure is eliminated. Such transformations can be filtered sensibly, and it is easy to compare one transformation to another. These representations have two applications. First, we can use these methods to automatically organize and display sets of closely related compounds such that any consistent local QSAR in a data set can be easily seen, the T-ANALYZE application. Second, we can suggest to a chemist how to change a molecule "on hand" to a more active one based on local QSAR for that activity, the T-MORPH application.