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Ligand Conformational and Solvation/Desolvation Free Energy in Protein-Ligand Complex Formation
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SYSNO ASEP 0367993 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Ligand Conformational and Solvation/Desolvation Free Energy in Protein-Ligand Complex Formation Author(s) Kolář, Michal (UOCHB-X) RID, ORCID
Fanfrlík, Jindřich (UOCHB-X) RID, ORCID
Hobza, Pavel (UOCHB-X) RID, ORCIDNumber of authors 3 Source Title Journal of Physical Chemistry B. - : American Chemical Society - ISSN 1520-6106
Roč. 115, č. 16 (2011), s. 4718-4724Number of pages 7 s. Language eng - English Country US - United States Keywords solvation free energy ; SMD ; HIV protease inhibitors Subject RIV CF - Physical ; Theoretical Chemistry R&D Projects LC512 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) GAP208/11/0295 GA ČR - Czech Science Foundation (CSF) CEZ AV0Z40550506 - UOCHB-X (2005-2011) UT WOS 000289697300020 DOI 10.1021/jp2010265 Annotation In this study, an extensive sampling of the conformational space of nine HIV-1 protease inhibitors was performed to estimate the uncertainty with which a single-conformation scoring scheme approximates the protein-ligand binding free energy. The SMD implicit solvation energy and gas-phase PM6-DH2 energy were calculated for a set of 1600 conformations of each ligand. The probability density functions of the energies were compared with the values obtained from the single-conformation approach and from a short ab initio molecular dynamics simulation. The relative uncertainty in the score within the set of nine inhibitors was calculated to be 3.5 kcal/mol and 2.7 kcal/mol for the single-conformation and short dynamics, respectively, which provides a valuable insight into the precision of rigid models in computer-aided drug design. 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 2012
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