Ligand Conformational and Solvation/Desolvation Free Energy in Protein-Ligand Complex Formation
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F11%3A00367993" target="_blank" >RIV/61388963:_____/11:00367993 - isvavai.cz</a>
Result on the web
<a href="http://dx.doi.org/10.1021/jp2010265" target="_blank" >http://dx.doi.org/10.1021/jp2010265</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/jp2010265" target="_blank" >10.1021/jp2010265</a>
Alternative languages
Result language
angličtina
Original language name
Ligand Conformational and Solvation/Desolvation Free Energy in Protein-Ligand Complex Formation
Original language description
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.
Czech name
—
Czech description
—
Classification
Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CF - Physical chemistry and theoretical chemistry
OECD FORD branch
—
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
Z - Vyzkumny zamer (s odkazem do CEZ)
Others
Publication year
2011
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Journal of Physical Chemistry B
ISSN
1520-6106
e-ISSN
—
Volume of the periodical
115
Issue of the periodical within the volume
16
Country of publishing house
US - UNITED STATES
Number of pages
7
Pages from-to
4718-4724
UT code for WoS article
000289697300020
EID of the result in the Scopus database
—