ci400094h_si_001.pdf (197.78 kB)
Application of the Docking Program SOL for CSAR Benchmark
journal contribution
posted on 2016-02-19, 00:00 authored by Alexey
V. Sulimov, Danil C. Kutov, Igor V. Oferkin, Ekaterina
V. Katkova, Vladimir B. SulimovThis paper is devoted to results
obtained by the docking program
SOL and the post-processing program DISCORE at the CSAR benchmark.
SOL and DISCORE programs are described. SOL is the original docking
program developed on the basis of the genetic algorithm, MMFF94 force
field, rigid protein, precalculated energy grid including desolvation
in the frame of simplified GB model, vdW, and electrostatic interactions
and taking into account the ligand internal strain energy. An important
SOL feature is the single- or multi-processor performance for up to
hundreds of CPUs. DISCORE improves the binding energy scoring by the
local energy optimization of the ligand docked pose and a simple linear
regression on the base of available experimental data. The docking
program SOL has demonstrated a good ability for correct ligand positioning
in the active sites of the tested proteins in most cases of CSAR exercises.
SOL and DISCORE have not demonstrated very exciting results on the
protein–ligand binding free energy estimation. Nevertheless,
for some target proteins, SOL and DISCORE were among the first in
prediction of inhibition activity. Ways to improve SOL and DISCORE
are discussed.