期刊
BIOORGANIC & MEDICINAL CHEMISTRY
卷 21, 期 6, 页码 1427-1430出版社
PERGAMON-ELSEVIER SCIENCE LTD
DOI: 10.1016/j.bmc.2012.10.040
关键词
Carbonic anhydrase; Molecular dynamics; Force field parameterization; OPLS-AA force field; Quantum chemistry
资金
- ANR [ANR-10-LABX-33]
The parameterization of carbonic anhydrase binding site in OPLS-AA force field was performed using quantum chemistry calculations. Both OH2 and OH forms of the binding site were considered, showing important differences in terms of atomic partial charges. Three different parameterization protocols were used, and the results obtained highlighted the importance of including an extended binding site in the charge calculation. The force field parameters were subsequently validated using standard molecular dynamics simulations. The results presented in this work should greatly facilitate the use of molecular dynamics simulations for studying the carbonic anhydrase, and more generally, the metallo-enzymes. (C) 2012 Elsevier Ltd. All rights reserved.
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