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Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations.
Nat Protoc. 2022 Apr;17(4):1114-1141. doi: 10.1038/s41596-021-00676-1. Epub 2022 Mar 11.
Nat Protoc. 2022.
PMID: 35277695
Free PMC article.
Review.
Hazardous Shortcuts in Standard Binding Free Energy Calculations.
Blazhynska M, Goulard Coderc de Lacam E, Chen H, Roux B, Chipot C.
Blazhynska M, et al.
J Phys Chem Lett. 2022 Jul 14;13(27):6250-6258. doi: 10.1021/acs.jpclett.2c01490. Epub 2022 Jun 30.
J Phys Chem Lett. 2022.
PMID: 35771686
Review.
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When the Dust Has Settled: Calculation of Binding Affinities from First Principles for SARS-CoV-2 Variants with Quantitative Accuracy.
Coderc de Lacam EG, Blazhynska M, Chen H, Gumbart JC, Chipot C.
Coderc de Lacam EG, et al. Among authors: blazhynska m.
J Chem Theory Comput. 2022 Oct 11;18(10):5890-5900. doi: 10.1021/acs.jctc.2c00604. Epub 2022 Sep 15.
J Chem Theory Comput. 2022.
PMID: 36108303
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A Rigorous Framework for Calculating Protein-Protein Binding Affinities in Membranes.
Blazhynska M, Gumbart JC, Chen H, Tajkhorshid E, Roux B, Chipot C.
Blazhynska M, et al.
J Chem Theory Comput. 2023 Dec 26;19(24):9077-9092. doi: 10.1021/acs.jctc.3c00941. Epub 2023 Dec 13.
J Chem Theory Comput. 2023.
PMID: 38091976
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Improving Speed and Affordability without Compromising Accuracy: Standard Binding Free-Energy Calculations Using an Enhanced Sampling Algorithm, Multiple-Time Stepping, and Hydrogen Mass Repartitioning.
Blazhynska M, Goulard Coderc de Lacam E, Chen H, Chipot C.
Blazhynska M, et al.
J Chem Theory Comput. 2023 Jun 13;19(11):3091-3101. doi: 10.1021/acs.jctc.3c00141. Epub 2023 May 17.
J Chem Theory Comput. 2023.
PMID: 37196198
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