A Reliable Docking/Scoring Scheme Based on the Semiempirical Quantum Mechanical PM6-DH2 Method Accurately Covering Dispersion and H-Bonding: HIV-1 Protease with 22 Ligands

0351836 - ÚOCHB 2011 RIV US eng J - Journal Article
Fanfrlík, Jindřich - Bronowska, A. K. - Řezáč, Jan - Přenosil, Ondřej - Konvalinka, Jan - Hobza, Pavel
A Reliable Docking/Scoring Scheme Based on the Semiempirical Quantum Mechanical PM6-DH2 Method Accurately Covering Dispersion and H-Bonding: HIV-1 Protease with 22 Ligands.
Journal of Physical Chemistry B. Roč. 114, č. 39 (2010), s. 12666-12678. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA MŠMT LC512; GA MŠMT 1M0508
Institutional research plan: CEZ:AV0Z40550506
Keywords : protein-ligand scoring * PM6-DH2 * HIV protease
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 3.603, year: 2010

In this study, we introduce a fast and reliable rescoring scheme for docked complexes based on a semiempirical quantum mechanical PM6-DH2 method. The method utilizes a PM6-based Hamiltonian with corrections for dispersion energy and hydrogen bonds. The total score is constructed as the sum of the PM6-DH2 interaction enthalpy, the empirical force field (AMBER) interaction entropy, and the sum of the deformation (PM6- DH2, SMD) and the desolvation (SMD) energies of the ligand. The main advantage of the procedure is the fact that we do not add any empirical parameter for either an individual component of the total score or an individual protein-ligand complex. This rescoring method is applied to a very challenging system, namely, the HIV-1 protease with a set of ligands.
Permanent Link: http://hdl.handle.net/11104/0006178