Аннотация:The novel docking algorithm is presented and it is applied to the
docking problem with flexible ligand and moveable protein atoms. The energy of
the protein-ligand complex is calculated in the frame of the MMFF94 force field
in vacuum. The conformation space of the system coordinates is formed by translations
and rotations of the ligand as a whole, by the ligand torsions and also by
Cartesian coordinates of the selected target protein atoms. The algorithm is realized
in the novel parallel docking SOL-P program and results of its performance
for a set of 30 protein-ligand complexes are presented. It is shown that mobility
of the protein atoms improves docking positioning accuracy. The SOL-P program
is able to perform docking of a flexible ligand into the active site of the target
protein with several dozen of protein moveable atoms – up to 157 degrees of
freedom.