The programs Phase and Catalyst HypoGen are compared for their performance in 
determining three-dimensional quantitative structure-activity relationships. 
Eight sets of compounds with measured activity were collected from the public 
literature and partitioned into suitable training and test sets by an automated 
procedure. A range of models is built with each program, and suggested parameter 
variations are investigated. The models are assessed by their ability to predict 
the activity of compounds in the test set, and it is demonstrated that the 
performance of Phase is better than or equal to that of Catalyst HypoGen, with 
the data sets and parameters used here. Additionally, compounds in two of the 
data sets are overlaid on crystallographic structures of similar ligands in 
complex with the target receptor, in order to guide pharmacophore generation by 
the two programs, but the resulting models do not perform better.