Scientific researchers of the Department of Medicinal Chemistry of the Institute of Molecular Biology and Genetics, the NAS of Ukraine, have developed the algorithm for pharmacophore model optimization and rescoring of pharmacophore screening results. The algorithm was written in the Java programming language, has a graphical interface and a system of parallelization. The application of algorithm allowed to increase the number of active compounds identified during pharmacophore screening and percent of correctly found active compounds in the top.