Suh D - Search Results

1

Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.

Radak BK, Chipot C, Suh D, Jo S, Jiang W, Phillips JC, Schulten K, Roux B. Radak BK, et al. Among authors: suh d. J Chem Theory Comput. 2017 Dec 12;13(12):5933-5944. doi: 10.1021/acs.jctc.7b00875. Epub 2017 Nov 22. J Chem Theory Comput. 2017. PMID: 29111720 Free PMC article.

2

Leveraging the Information from Markov State Models To Improve the Convergence of Umbrella Sampling Simulations.

Jo S, Suh D, He Z, Chipot C, Roux B. Jo S, et al. Among authors: suh d. J Phys Chem B. 2016 Aug 25;120(33):8733-42. doi: 10.1021/acs.jpcb.6b05125. Epub 2016 Aug 3. J Phys Chem B. 2016. PMID: 27409349

3

Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics-Monte Carlo propagator.

Suh D, Radak BK, Chipot C, Roux B. Suh D, et al. J Chem Phys. 2018 Jan 7;148(1):014101. doi: 10.1063/1.5004154. J Chem Phys. 2018. PMID: 29306299

4

A generalized linear response framework for expanded ensemble and replica exchange simulations.

Radak BK, Suh D, Roux B. Radak BK, et al. Among authors: suh d. J Chem Phys. 2018 Aug 21;149(7):072315. doi: 10.1063/1.5027494. J Chem Phys. 2018. PMID: 30134700 Free PMC article.

5

Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages.

Loeffler HH, Bosisio S, Duarte Ramos Matos G, Suh D, Roux B, Mobley DL, Michel J. Loeffler HH, et al. Among authors: suh d. J Chem Theory Comput. 2018 Nov 13;14(11):5567-5582. doi: 10.1021/acs.jctc.8b00544. Epub 2018 Oct 22. J Chem Theory Comput. 2018. PMID: 30289712

6

Correction to Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.

Radak BK, Chipot C, Suh D, Jo S, Jiang W, Phillips JC, Schulten K, Roux B. Radak BK, et al. Among authors: suh d. J Chem Theory Comput. 2018 Dec 11;14(12):6748-6749. doi: 10.1021/acs.jctc.8b01075. Epub 2018 Nov 27. J Chem Theory Comput. 2018. PMID: 30480445 No abstract available.

7

String Method for Protein-Protein Binding Free-Energy Calculations.

Suh D, Jo S, Jiang W, Chipot C, Roux B. Suh D, et al. J Chem Theory Comput. 2019 Nov 12;15(11):5829-5844. doi: 10.1021/acs.jctc.9b00499. Epub 2019 Oct 31. J Chem Theory Comput. 2019. PMID: 31593627

8

CHARMM-GUI QM/MM Interfacer for a Quantum Mechanical and Molecular Mechanical (QM/MM) Simulation Setup: 1. Semiempirical Methods.

Suh D, Arattu Thodika AR, Kim S, Nam K, Im W. Suh D, et al. J Chem Theory Comput. 2024 Jun 25;20(12):5337-5351. doi: 10.1021/acs.jctc.4c00439. Epub 2024 Jun 10. J Chem Theory Comput. 2024. PMID: 38856971 Free PMC article.

9

Advances in Molecular Dynamics Simulations and Enhanced Sampling Methods for the Study of Protein Systems.

Lazim R, Suh D, Choi S. Lazim R, et al. Among authors: suh d. Int J Mol Sci. 2020 Sep 1;21(17):6339. doi: 10.3390/ijms21176339. Int J Mol Sci. 2020. PMID: 32882859 Free PMC article. Review.

10

CHARMM-GUI Implicit Solvent Modeler for Various Generalized Born Models in Different Simulation Programs.

Wang KW, Lee J, Zhang H, Suh D, Im W. Wang KW, et al. Among authors: suh d. J Phys Chem B. 2022 Sep 29;126(38):7354-7364. doi: 10.1021/acs.jpcb.2c05294. Epub 2022 Sep 18. J Phys Chem B. 2022. PMID: 36117287 Free PMC article.

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