Jo S - Search Results

1

Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model.

Das A, Gur M, Cheng MH, Jo S, Bahar I, Roux B. Das A, et al. Among authors: jo s. PLoS Comput Biol. 2014 Apr 3;10(4):e1003521. doi: 10.1371/journal.pcbi.1003521. eCollection 2014 Apr. PLoS Comput Biol. 2014. PMID: 24699246 Free PMC article.

2

Efficient Determination of Relative Entropy Using Combined Temperature and Hamiltonian Replica-Exchange Molecular Dynamics.

Jo S, Chipot C, Roux B. Jo S, et al. J Chem Theory Comput. 2015 May 12;11(5):2234-44. doi: 10.1021/ct501034w. Epub 2015 Apr 21. J Chem Theory Comput. 2015. PMID: 26574422

3

CHARMM-GUI 10 years for biomolecular modeling and simulation.

Jo S, Cheng X, Lee J, Kim S, Park SJ, Patel DS, Beaven AH, Lee KI, Rui H, Park S, Lee HS, Roux B, MacKerell AD Jr, Klauda JB, Qi Y, Im W. Jo S, et al. J Comput Chem. 2017 Jun 5;38(15):1114-1124. doi: 10.1002/jcc.24660. Epub 2016 Nov 14. J Comput Chem. 2017. PMID: 27862047 Free PMC article. Review.

4

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

Suh D, Jo S, Jiang W, Chipot C, Roux B. Suh D, et al. Among authors: jo s. 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

5

CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues.

Jo S, Cheng X, Islam SM, Huang L, Rui H, Zhu A, Lee HS, Qi Y, Han W, Vanommeslaeghe K, MacKerell AD Jr, Roux B, Im W. Jo S, et al. Adv Protein Chem Struct Biol. 2014;96:235-65. doi: 10.1016/bs.apcsb.2014.06.002. Epub 2014 Aug 24. Adv Protein Chem Struct Biol. 2014. PMID: 25443960 Free PMC article. Review.

6

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. 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

7

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: jo s. 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.

8

Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis.

Jiang W, Thirman J, Jo S, Roux B. Jiang W, et al. Among authors: jo s. J Phys Chem B. 2018 Oct 18;122(41):9435-9442. doi: 10.1021/acs.jpcb.8b03277. Epub 2018 Oct 3. J Phys Chem B. 2018. PMID: 30253098 Free PMC article.

9

Web interface for Brownian dynamics simulation of ion transport and its applications to beta-barrel pores.

Lee KI, Jo S, Rui H, Egwolf B, Roux B, Pastor RW, Im W. Lee KI, et al. Among authors: jo s. J Comput Chem. 2012 Jan 30;33(3):331-9. doi: 10.1002/jcc.21952. Epub 2011 Nov 21. J Comput Chem. 2012. PMID: 22102176 Free PMC article.

10

CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application.

Jo S, Jiang W, Lee HS, Roux B, Im W. Jo S, et al. J Chem Inf Model. 2013 Jan 28;53(1):267-77. doi: 10.1021/ci300505n. Epub 2012 Dec 20. J Chem Inf Model. 2013. PMID: 23205773 Free PMC article.

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