An algorithm of assigning the force parameters to atoms of organic molecules and proteins in the framework of the MMFF94 force field

Abstract

The FARS (Fire Algorithm for Rings Search) algorithm of assigning the force parameters for atoms of organic molecules and proteins in the framework of the MMFF94 force field is considered. The algorithm is developed for solving the problem of virtual screening of molecules from databases in order to select those of them that interact with a target protein in the best way. The parameter values assigned by the FARS algorithm and by the CHARMM algorithm for compounds from the NCI_Diversity database are compared. The FARS algorithm is included into the Keenbase Web-oriented program complex developed specially for the problem of virtual screening. The FARS algorithm was successfully used in the course of a computer experiment for searching the inhibitors corresponding to given proteins on the basis of distributed computing technologies. This experiment was performed with the use of high-performance cluster systems installed at the Research Computer Center of Moscow State University and at the South Ural State University.