Drug Designing: Open Access
Open Access

Is it possible to improve considerably the accuracy of docking programs?

International Conference and Expo on Drug Discovery & Designing

August 11-13, 2015 Frankfurt, Germany

Vladimir Sulimov

Scientific Tracks Abstracts: Drug Des

Abstract :

Protein-ligand binding free energy calculation is one of the key problems for molecular modeling in the computer-aided
structural based drug design. Only with accuracy better than 1 kcal/mol of the protein-ligand binding free energy
calculations it is possible to perform the rational inhibitor optimization on the basis of computer modeling. However such high
accuracy has not been reached yet for a randomly selected target protein by any docking programs. It is not surprising because
this accuracy depends on many interrelated factors in a complicated manner. Those factors are: the force field describing interand
intra-molecular interactions, the water model, the target protein and ligand models, method and approximations of the
free energy calculation, algorithms of calculations and computing resources concentrated on solving the docking problem for
one protein-ligand pair, etc. The results of binding energy calculations within the multi-well approximation (protein-ligand
and free ligand low energy local minima spectra are taken into account when the binding energy is calculated) will be presented
for a set of protein-ligand complexes using MMFF94 force field, quantum-chemical method PM7 and implicit water models.
Comparison of calculated and experimental energies is presented. The roles of the ligand strain energy, the de-solvation energy
and the ligand vibrations are discussed. The broad discussion of the subject is invited.

Biography :

Vladimir Sulimov has completed his from Lomonosov Moscow State University in 1979 and he received the degree Doctor of Sciences in Physics and Mathematics
in 1997 from Prokhorov General Physics Institute. He is the Head of the Lab at Research Computer Center of Lomonosov Moscow State University. He has
published more than 220 papers in reputed journals with 40 years of theoretical research. His recent research activities are molecular modeling in structural-based
drug design, development of docking programs and their application for new inhibitors design. He is Founder and CEO of private Russian research company
Dimonta, Ltd.