Nerukh D - Search Results

1

Constant pH molecular dynamics of porcine circovirus 2 capsid protein reveals a mechanism for capsid assembly.

Tarasova E, Okimoto N, Feng S, Nerukh D, Khayat R, Taiji M. Tarasova E, et al. Among authors: nerukh d. Phys Chem Chem Phys. 2021 Nov 10;23(43):24617-24626. doi: 10.1039/d1cp02874j. Phys Chem Chem Phys. 2021. PMID: 34726674 Free PMC article.

2

Visualising and controlling the flow in biomolecular systems at and between multiple scales: from atoms to hydrodynamics at different locations in time and space.

Pavlov E, Taiji M, Scukins A, Markesteijn A, Karabasov S, Nerukh D. Pavlov E, et al. Among authors: nerukh d. Faraday Discuss. 2014;169:285-302. doi: 10.1039/c3fd00159h. Epub 2014 Jun 17. Faraday Discuss. 2014. PMID: 25340552

3

Ligand Diffusion on Protein Surface Observed in Molecular Dynamics Simulation.

Nerukh D, Okimoto N, Suenaga A, Taiji M. Nerukh D, et al. J Phys Chem Lett. 2012 Dec 6;3(23):3476-9. doi: 10.1021/jz301635h. Epub 2012 Nov 14. J Phys Chem Lett. 2012. PMID: 26290975

4

All-Atom Molecular Dynamics Simulations of Entire Virus Capsid Reveal the Role of Ion Distribution in Capsid's Stability.

Tarasova E, Farafonov V, Khayat R, Okimoto N, Komatsu TS, Taiji M, Nerukh D. Tarasova E, et al. Among authors: nerukh d. J Phys Chem Lett. 2017 Feb 16;8(4):779-784. doi: 10.1021/acs.jpclett.6b02759. Epub 2017 Feb 1. J Phys Chem Lett. 2017. PMID: 28129688 Free PMC article.

5

All-Atom Molecular Dynamics Simulations of Whole Viruses.

Tarasova E, Nerukh D. Tarasova E, et al. Among authors: nerukh d. J Phys Chem Lett. 2018 Oct 4;9(19):5805-5809. doi: 10.1021/acs.jpclett.8b02298. Epub 2018 Sep 24. J Phys Chem Lett. 2018. PMID: 30230849

6

Sensitivity of peptide conformational dynamics on clustering of a classical molecular dynamics trajectory.

Jensen CH, Nerukh D, Glen RC. Jensen CH, et al. Among authors: nerukh d. J Chem Phys. 2008 Mar 21;128(11):115107. doi: 10.1063/1.2838980. J Chem Phys. 2008. PMID: 18361622

7

Identifying and correcting non-Markov states in peptide conformational dynamics.

Nerukh D, Jensen CH, Glen RC. Nerukh D, et al. J Chem Phys. 2010 Feb 28;132(8):084104. doi: 10.1063/1.3328781. J Chem Phys. 2010. PMID: 20192287

8

Self-assembly of trehalose molecules on a lysozyme surface: the broken glass hypothesis.

Fedorov MV, Goodman JM, Nerukh D, Schumm S. Fedorov MV, et al. Among authors: nerukh d. Phys Chem Chem Phys. 2011 Feb 14;13(6):2294-9. doi: 10.1039/c0cp01705a. Epub 2010 Nov 29. Phys Chem Chem Phys. 2011. PMID: 21116551

9

Protein-Ligand Dissociation Rate Constant from All-Atom Simulation.

Maximova E, Postnikov EB, Lavrova AI, Farafonov V, Nerukh D. Maximova E, et al. Among authors: nerukh d. J Phys Chem Lett. 2021 Nov 4;12(43):10631-10636. doi: 10.1021/acs.jpclett.1c02952. Epub 2021 Oct 27. J Phys Chem Lett. 2021. PMID: 34704768

10

Exploring the mechanism of action of spirooxindoles as a class of CDK2 inhibitors: a structure-based computational approach.

Abdjan MI, Shafiq M, Nerukh D, Nur-E-Alam M, Ul-Haq Z. Abdjan MI, et al. Among authors: nerukh d. Phys Chem Chem Phys. 2024 Jun 6;26(22):16139-16152. doi: 10.1039/d4cp00844h. Phys Chem Chem Phys. 2024. PMID: 38787638

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