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Benchmarking of Semiempirical Quantum-Mechanical Methods on Systems Relevant to Computer-Aided Drug Design
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SYSNO ASEP 0523808 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Benchmarking of Semiempirical Quantum-Mechanical Methods on Systems Relevant to Computer-Aided Drug Design Author(s) Kříž, Kristian (UOCHB-X) ORCID
Řezáč, Jan (UOCHB-X) RID, ORCIDSource Title Journal of Chemical Information and Modeling. - : American Chemical Society - ISSN 1549-9596
Roč. 60, č. 3 (2020), s. 1453-1460Number of pages 8 s. Language eng - English Country US - United States Keywords protein-ligand complexes ; interaction energies ; NDDO approximations Subject RIV CF - Physical ; Theoretical Chemistry OECD category Physical chemistry R&D Projects EF16_019/0000729 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) GA19-13905S GA ČR - Czech Science Foundation (CSF) Method of publishing Open access Institutional support UOCHB-X - RVO:61388963 UT WOS 000526390800036 EID SCOPUS 85082148168 DOI 10.1021/acs.jcim.9b01171 Annotation The semiempirical quantum mechanical (SQM) methods used in drug design are commonly parametrized and tested on data sets of systems that may not be representative models for drug-biomolecule interactions in terms of both size and chemical composition. This is addressed here with a new benchmark data set, PLF547, derived from protein-ligand complexes, consisting of complexes of ligands with protein fragments (such as amino-acid side chains), with interaction energies based on MP2-F12 and DLPNO-CCSD(T) calculations. From these, composite benchmark interaction energies are also built for complexes of the ligand with the complete active site of the protein (PLA15 data set). These data sets are used to test multiple SQM methods with corrections for noncovalent interactions, the role of the solvation model in the calculations is tested as well. Workplace Institute of Organic Chemistry and Biochemistry Contact asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Jana Procházková, Tel.: 220 183 418 Year of Publishing 2021 Electronic address https://pubs.acs.org/doi/10.1021/acs.jcim.9b01171
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