John H. Van Drie

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A new method for analyzing a structure-activity relationship is proposed. By use of a simple quantitative index, one can readily identify "structure-activity cliffs": pairs of molecules which are most similar but have the largest change in activity. We show how this provides a graphical representation of the entire SAR, in a way that allows the salient(More)
We introduce the notion of structure-activity landscape index (SALI) curves as a way to assess a model and a modeling protocol, applied to structure-activity relationships. We start from our earlier work [ J. Chem. Inf. Model., 2008, 48, 646-658], where we show how to study a structure-activity relationship pairwise, based on the notion of "activity(More)
ALADDIN is a computer program for the design or recognition of compounds that meet geometric, steric, and substructural criteria. ALADDIN searches a database of three-dimensional structures, marks atoms that meet substructural criteria, evaluates geometric criteria, and prepares a number of files that are input for molecular modification and coordinate(More)
Pharmacophores have had their utility demonstrated in many ways. They figure most prominently in drug discovery efforts where no structure of the macromolecular target is available (either experimentally via X-ray crystallography or NMR, or by homology modeling), where pharmacophores function as low-resolution models to help understand the SAR and drive the(More)