Zinovjev K - Search Results

1

Improved Description of Environment and Vibronic Effects with Electrostatically Embedded ML Potentials.

Zinovjev K, Curutchet C. Zinovjev K, et al. J Phys Chem Lett. 2025 Jan 23;16(3):774-781. doi: 10.1021/acs.jpclett.4c02949. Epub 2025 Jan 13. J Phys Chem Lett. 2025. PMID: 39804789

2

Influence of Wobbling Tryptophan and Mutations on PET Degradation Explored by QM/MM Free Energy Calculations.

Jäckering A, van der Kamp M, Strodel B, Zinovjev K. Jäckering A, et al. Among authors: zinovjev k. J Chem Inf Model. 2024 Oct 14;64(19):7544-7554. doi: 10.1021/acs.jcim.4c00776. Epub 2024 Sep 29. J Chem Inf Model. 2024. PMID: 39344272 Free PMC article.

3

emle-engine: A Flexible Electrostatic Machine Learning Embedding Package for Multiscale Molecular Dynamics Simulations.

Zinovjev K, Hedges L, Montagud Andreu R, Woods C, Tuñón I, van der Kamp MW. Zinovjev K, et al. J Chem Theory Comput. 2024 Jun 11;20(11):4514-4522. doi: 10.1021/acs.jctc.4c00248. Epub 2024 May 28. J Chem Theory Comput. 2024. PMID: 38804055 Free PMC article.

4

Activation and friction in enzymatic loop opening and closing dynamics.

Zinovjev K, Guénon P, Ramos-Guzmán CA, Ruiz-Pernía JJ, Laage D, Tuñón I. Zinovjev K, et al. Nat Commun. 2024 Mar 20;15(1):2490. doi: 10.1038/s41467-024-46723-9. Nat Commun. 2024. PMID: 38509080 Free PMC article.

5

4-Thiaproline accelerates the slow folding phase of proteins containing cis prolines in the native state by two orders of magnitude.

Loughlin JO, Zinovjev K, Napolitano S, van der Kamp M, Rubini M. Loughlin JO, et al. Among authors: zinovjev k. Protein Sci. 2024 Feb;33(2):e4877. doi: 10.1002/pro.4877. Protein Sci. 2024. PMID: 38115231 Free PMC article.

6

Conformational Changes and ATP Hydrolysis in Zika Helicase: The Molecular Basis of a Biomolecular Motor Unveiled by Multiscale Simulations.

García-Martínez A, Zinovjev K, Ruiz-Pernía JJ, Tuñón I. García-Martínez A, et al. Among authors: zinovjev k. J Am Chem Soc. 2023 Nov 15;145(45):24809-24819. doi: 10.1021/jacs.3c09015. Epub 2023 Nov 3. J Am Chem Soc. 2023. PMID: 37921592 Free PMC article.

7

Free energy along drug-protein binding pathways interactively sampled in virtual reality.

Deeks HM, Zinovjev K, Barnoud J, Mulholland AJ, van der Kamp MW, Glowacki DR. Deeks HM, et al. Among authors: zinovjev k. Sci Rep. 2023 Oct 4;13(1):16665. doi: 10.1038/s41598-023-43523-x. Sci Rep. 2023. PMID: 37794083 Free PMC article.

8

Elucidation of the Active Form and Reaction Mechanism in Human Asparaginase Type III Using Multiscale Simulations.

Andjelkovic M, Zinovjev K, Ramos-Guzmán CA, Ruiz-Pernía JJ, Tuñón I. Andjelkovic M, et al. Among authors: zinovjev k. J Chem Inf Model. 2023 Sep 11;63(17):5676-5688. doi: 10.1021/acs.jcim.3c00900. Epub 2023 Aug 27. J Chem Inf Model. 2023. PMID: 37635309 Free PMC article.

9

Unveiling the Mechanistic Singularities of Caspases: A Computational Analysis of the Reaction Mechanism in Human Caspase-1.

Ramos-Guzmán CA, Ruiz-Pernía JJ, Zinovjev K, Tuñón I. Ramos-Guzmán CA, et al. Among authors: zinovjev k. ACS Catal. 2023 Mar 15;13(7):4348-4361. doi: 10.1021/acscatal.3c00037. eCollection 2023 Apr 7. ACS Catal. 2023. PMID: 37066044 Free PMC article.

10

Tautomer-Specific Deacylation and Ω-Loop Flexibility Explain the Carbapenem-Hydrolyzing Broad-Spectrum Activity of the KPC-2 β-Lactamase.

Tooke CL, Hinchliffe P, Beer M, Zinovjev K, Colenso CK, Schofield CJ, Mulholland AJ, Spencer J. Tooke CL, et al. Among authors: zinovjev k. J Am Chem Soc. 2023 Apr 5;145(13):7166-7180. doi: 10.1021/jacs.2c12123. Epub 2023 Mar 27. J Am Chem Soc. 2023. PMID: 36972204 Free PMC article.

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