Gumbart JC - Search Results

1

Parametrization of macrolide antibiotics using the force field toolkit.

Pavlova A, Gumbart JC. Pavlova A, et al. Among authors: gumbart jc. J Comput Chem. 2015 Oct 15;36(27):2052-63. doi: 10.1002/jcc.24043. Epub 2015 Aug 17. J Comput Chem. 2015. PMID: 26280362 Free PMC article.

2

Rapid parameterization of small molecules using the Force Field Toolkit.

Mayne CG, Saam J, Schulten K, Tajkhorshid E, Gumbart JC. Mayne CG, et al. Among authors: gumbart jc. J Comput Chem. 2013 Dec 15;34(32):2757-70. doi: 10.1002/jcc.23422. Epub 2013 Sep 2. J Comput Chem. 2013. PMID: 24000174 Free PMC article.

3

Escherichia coli peptidoglycan structure and mechanics as predicted by atomic-scale simulations.

Gumbart JC, Beeby M, Jensen GJ, Roux B. Gumbart JC, et al. PLoS Comput Biol. 2014 Feb 20;10(2):e1003475. doi: 10.1371/journal.pcbi.1003475. eCollection 2014 Feb. PLoS Comput Biol. 2014. PMID: 24586129 Free PMC article.

4

Living on the edge: Simulations of bacterial outer-membrane proteins.

Pavlova A, Hwang H, Lundquist K, Balusek C, Gumbart JC. Pavlova A, et al. Among authors: gumbart jc. Biochim Biophys Acta. 2016 Jul;1858(7 Pt B):1753-9. doi: 10.1016/j.bbamem.2016.01.020. Epub 2016 Jan 28. Biochim Biophys Acta. 2016. PMID: 26826270 Free article. Review.

5

Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds.

Lee CT, Comer J, Herndon C, Leung N, Pavlova A, Swift RV, Tung C, Rowley CN, Amaro RE, Chipot C, Wang Y, Gumbart JC. Lee CT, et al. Among authors: gumbart jc. J Chem Inf Model. 2016 Apr 25;56(4):721-33. doi: 10.1021/acs.jcim.6b00022. Epub 2016 Apr 14. J Chem Inf Model. 2016. PMID: 27043429 Free PMC article.

6

Redox-Driven Conformational Dynamics in a Photosystem-II-Inspired β-Hairpin Maquette Determined through Spectroscopy and Simulation.

Hwang H, McCaslin TG, Hazel A, Pagba CV, Nevin CM, Pavlova A, Barry BA, Gumbart JC. Hwang H, et al. Among authors: gumbart jc. J Phys Chem B. 2017 Apr 20;121(15):3536-3545. doi: 10.1021/acs.jpcb.6b09481. Epub 2017 Feb 13. J Phys Chem B. 2017. PMID: 28145121

7

Toward the rational design of macrolide antibiotics to combat resistance.

Pavlova A, Parks JM, Oyelere AK, Gumbart JC. Pavlova A, et al. Among authors: gumbart jc. Chem Biol Drug Des. 2017 Nov;90(5):641-652. doi: 10.1111/cbdd.13004. Epub 2017 May 16. Chem Biol Drug Des. 2017. PMID: 28419786

8

Producing membrane proteins one simulation at a time.

Gumbart JC. Gumbart JC. J Biol Chem. 2017 Nov 24;292(47):19546-19547. doi: 10.1074/jbc.H117.813469. J Biol Chem. 2017. PMID: 29175817 Free PMC article.

9

Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations.

Pavlova A, Parks JM, Gumbart JC. Pavlova A, et al. Among authors: gumbart jc. J Chem Theory Comput. 2018 Feb 13;14(2):784-798. doi: 10.1021/acs.jctc.7b01236. Epub 2018 Feb 1. J Chem Theory Comput. 2018. PMID: 29334459 Free PMC article.

10

Accelerating Membrane Simulations with Hydrogen Mass Repartitioning.

Balusek C, Hwang H, Lau CH, Lundquist K, Hazel A, Pavlova A, Lynch DL, Reggio PH, Wang Y, Gumbart JC. Balusek C, et al. Among authors: gumbart jc. J Chem Theory Comput. 2019 Aug 13;15(8):4673-4686. doi: 10.1021/acs.jctc.9b00160. Epub 2019 Jul 2. J Chem Theory Comput. 2019. PMID: 31265271 Free PMC article.

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