MOLGEN is a comprehensive molecular modeling package that runs on personal computers and allows building, drawing, storing, and comparison of molecular structures. The system contains modules for geometry optimization and conformational analysis, and modules for calculation and description of lipophilicity and electrostatic potentials and for their three-dimensional matching based on gnomonic projection. Described here are a systematic conformation search running on PCs and a new approach to 3D similarity analysis of lipophilic potentials. The drug design applicability of the program is further enhanced by database facilities for retrieving and storing any structure data sets. The program features and examples of its applications are presented.