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How Reproducible Are QM/MM Simulations?: Lessons from Computational Studies of the Covalent Inhibition of the SARS-CoV-2 Main Protease by Carmofurстатья
Статья опубликована в высокорейтинговом журнале
Статья опубликована в журнале из списка Web of Science и/или Scopus- Авторы: Giudetti Goran, Polyakov Igor, Grigorenko Bella L., Faraji Shirin, Nemukhin Alexander V., Krylov Anna I.
- Журнал: Journal of Chemical Theory and Computation
- Том: 18
- Номер: 8
- Год издания: 2022
- Издательство: American Chemical Society
- Местоположение издательства: United States
- Первая страница: 5056
- Последняя страница: 5067
- DOI: 10.1021/acs.jctc.2c00286
- Аннотация: This work explores the level of transparency in reporting thedetails of computational protocols that is required for practical reproducibilityof quantum mechanics/molecular mechanics (QM/MM) simulations. Usingthe reaction of an essential SARS-CoV-2 enzyme (the main protease) with acovalent inhibitor (carmofur) as a test case of chemical reactions inbiomolecules, we carried out QM/MM calculations to determine thestructures and energies of the reactants, the product, and the transitionstate/intermediate using analogous QM/MM models implemented in twosoftware packages, NWChem and Q-Chem. Our main benchmarking goal wasto reproduce the key energetics computed with the two packages. Our resultsindicate that quantitative agreement (within the numerical thresholds used incalculations) is difficult to achieve. We show that rather minor details of QM/MM simulations must be reported in order to ensure the reproducibility of theresults and offer suggestions toward developing practical guidelines for reporting the results of biosimulations.
- Добавил в систему: Немухин Александр Владимирович