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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

SYSNO ASEP	0351836
Document Type	J - Journal Article
R&D Document Type	Journal Article
Subsidiary J	Článek ve WOS
Title	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
Author(s)	Fanfrlík, Jindřich (UOCHB-X)_{RID, ORCID} Bronowska, A. K. (DE) Řezáč, Jan (UOCHB-X)_{RID, ORCID} Přenosil, Ondřej (UOCHB-X) Konvalinka, Jan (UOCHB-X)_{RID, ORCID} Hobza, Pavel (UOCHB-X)_{RID, ORCID}
Number of authors	6
Source Title	Journal of Physical Chemistry B. - : American Chemical Society - ISSN 1520-6106 Roč. 114, č. 39 (2010), s. 12666-12678
Number of pages	13 s.
Language	eng - English
Country	US - United States
Keywords	protein-ligand scoring ; PM6-DH2 ; HIV protease
Subject RIV	CF - Physical ; Theoretical Chemistry
R&D Projects	LC512 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
	1M0508 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
CEZ	AV0Z40550506 - UOCHB-X (2005-2011)
UT WOS	000282209900029
DOI	10.1021/jp1032965
Annotation	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.
Workplace	Institute of Organic Chemistry and Biochemistry
Contact	asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Viktorie Chládková, Tel.: 232 002 434
Year of Publishing	2011

Number of the records: 1