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Items: 1 to 20 of 42

1.

Folding free energy landscapes of β-sheets with non-polarizable and polarizable CHARMM force fields.

Hazel AJ, Walters ET, Rowley CN, Gumbart JC.

J Chem Phys. 2018 Aug 21;149(7):072317. doi: 10.1063/1.5025951.

PMID:
30134731
2.

C-terminal kink formation is required for lateral gating in BamA.

Lundquist K, Bakelar J, Noinaj N, Gumbart JC.

Proc Natl Acad Sci U S A. 2018 Aug 21;115(34):E7942-E7949. doi: 10.1073/pnas.1722530115. Epub 2018 Aug 7.

PMID:
30087180
3.

Correction to: Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method.

Gumbart JC, Ulmschneider MB, Hazel A, White SH, Ulmschneider JP.

J Membr Biol. 2018 Jun;251(3):357. doi: 10.1007/s00232-018-0038-7.

PMID:
29943127
4.

Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method.

Gumbart JC, Ulmschneider MB, Hazel A, White SH, Ulmschneider JP.

J Membr Biol. 2018 Jun;251(3):345-356. doi: 10.1007/s00232-018-0026-y. Epub 2018 Mar 8. Erratum in: J Membr Biol. 2018 Jun 25;:.

PMID:
29520628
5.

BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations.

Fu H, Gumbart JC, Chen H, Shao X, Cai W, Chipot C.

J Chem Inf Model. 2018 Mar 26;58(3):556-560. doi: 10.1021/acs.jcim.7b00695. Epub 2018 Feb 16.

PMID:
29405709
6.

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

Pavlova A, Parks JM, Gumbart JC.

J Chem Theory Comput. 2018 Feb 13;14(2):784-798. doi: 10.1021/acs.jctc.7b01236. Epub 2018 Feb 1.

PMID:
29334459
7.

Producing membrane proteins one simulation at a time.

Gumbart JC.

J Biol Chem. 2017 Nov 24;292(47):19546-19547. doi: 10.1074/jbc.H117.813469.

8.

Structure and Misfolding of the Flexible Tripartite Coiled-Coil Domain of Glaucoma-Associated Myocilin.

Hill SE, Nguyen E, Donegan RK, Patterson-Orazem AC, Hazel A, Gumbart JC, Lieberman RL.

Structure. 2017 Nov 7;25(11):1697-1707.e5. doi: 10.1016/j.str.2017.09.008.

PMID:
29056483
9.

Structural basis for substrate selection by the translocation and assembly module of the β-barrel assembly machinery.

Bamert RS, Lundquist K, Hwang H, Webb CT, Shiota T, Stubenrauch CJ, Belousoff MJ, Goode RJA, Schittenhelm RB, Zimmerman R, Jung M, Gumbart JC, Lithgow T.

Mol Microbiol. 2017 Oct;106(1):142-156. doi: 10.1111/mmi.13757. Epub 2017 Aug 9.

PMID:
28752534
10.

Toward the rational design of macrolide antibiotics to combat resistance.

Pavlova A, Parks JM, Oyelere AK, Gumbart JC.

Chem Biol Drug Des. 2017 Nov;90(5):641-652. doi: 10.1111/cbdd.13004. Epub 2017 May 16.

PMID:
28419786
11.

The β-barrel assembly machinery in motion.

Noinaj N, Gumbart JC, Buchanan SK.

Nat Rev Microbiol. 2017 Apr;15(4):197-204. doi: 10.1038/nrmicro.2016.191. Epub 2017 Feb 20. Review.

12.

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.

J Phys Chem B. 2017 Apr 20;121(15):3536-3545. doi: 10.1021/acs.jpcb.6b09481. Epub 2017 Feb 13.

PMID:
28145121
13.

Role of the Native Outer-Membrane Environment on the Transporter BtuB.

Balusek C, Gumbart JC.

Biophys J. 2016 Oct 4;111(7):1409-1417. doi: 10.1016/j.bpj.2016.08.033.

14.

Coarse-Grained Molecular Dynamics Simulations of the Bacterial Cell Wall.

Nguyen LT, Gumbart JC, Jensen GJ.

Methods Mol Biol. 2016;1440:247-70. doi: 10.1007/978-1-4939-3676-2_18.

PMID:
27311677
15.

DNA Scrunching in the Packaging of Viral Genomes.

Waters JT, Kim HD, Gumbart JC, Lu XJ, Harvey SC.

J Phys Chem B. 2016 Jul 7;120(26):6200-7. doi: 10.1021/acs.jpcb.6b02149. Epub 2016 May 26.

16.

Structural and Functional Characterization of the LPS Transporter LptDE from Gram-Negative Pathogens.

Botos I, Majdalani N, Mayclin SJ, McCarthy JG, Lundquist K, Wojtowicz D, Barnard TJ, Gumbart JC, Buchanan SK.

Structure. 2016 Jun 7;24(6):965-976. doi: 10.1016/j.str.2016.03.026. Epub 2016 May 5.

17.

Transitions of Double-Stranded DNA Between the A- and B-Forms.

Waters JT, Lu XJ, Galindo-Murillo R, Gumbart JC, Kim HD, Cheatham TE 3rd, Harvey SC.

J Phys Chem B. 2016 Aug 25;120(33):8449-56. doi: 10.1021/acs.jpcb.6b02155. Epub 2016 May 11.

18.

Membrane proteins: Where theory meets experiment.

Gumbart JC, Noskov S.

Biochim Biophys Acta. 2016 Jul;1858(7 Pt B):1553-5. doi: 10.1016/j.bbamem.2016.04.007. Epub 2016 Apr 16. No abstract available.

19.

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.

J Chem Inf Model. 2016 Apr 25;56(4):721-33. doi: 10.1021/acs.jcim.6b00022. Epub 2016 Apr 14.

20.

Decrypting protein insertion through the translocon with free-energy calculations.

Gumbart JC, Chipot C.

Biochim Biophys Acta. 2016 Jul;1858(7 Pt B):1663-71. doi: 10.1016/j.bbamem.2016.02.017. Epub 2016 Feb 16. Review.

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