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Scalable molecular dynamics with NAMD.
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K. Phillips JC, et al. Among authors: gumbart j. J Comput Chem. 2005 Dec;26(16):1781-802. doi: 10.1002/jcc.20289. J Comput Chem. 2005. PMID: 16222654 Free PMC article.
Molecular dynamics simulations of proteins in lipid bilayers.
Gumbart J, Wang Y, Aksimentiev A, Tajkhorshid E, Schulten K. Gumbart J, et al. Curr Opin Struct Biol. 2005 Aug;15(4):423-31. doi: 10.1016/j.sbi.2005.07.007. Curr Opin Struct Biol. 2005. PMID: 16043343 Free PMC article. Review.
Molecular dynamics studies of the archaeal translocon.
Gumbart J, Schulten K. Gumbart J, et al. Biophys J. 2006 Apr 1;90(7):2356-67. doi: 10.1529/biophysj.105.075291. Epub 2006 Jan 13. Biophys J. 2006. PMID: 16415058 Free PMC article.
Mechanics of force propagation in TonB-dependent outer membrane transport.
Gumbart J, Wiener MC, Tajkhorshid E. Gumbart J, et al. Biophys J. 2007 Jul 15;93(2):496-504. doi: 10.1529/biophysj.107.104158. Epub 2007 Apr 20. Biophys J. 2007. PMID: 17449669 Free PMC article.
Structural determinants of lateral gate opening in the protein translocon.
Gumbart J, Schulten K. Gumbart J, et al. Biochemistry. 2007 Oct 2;46(39):11147-57. doi: 10.1021/bi700835d. Epub 2007 Aug 31. Biochemistry. 2007. PMID: 17760424
The roles of pore ring and plug in the SecY protein-conducting channel.
Gumbart J, Schulten K. Gumbart J, et al. J Gen Physiol. 2008 Dec;132(6):709-19. doi: 10.1085/jgp.200810062. Epub 2008 Nov 10. J Gen Physiol. 2008. PMID: 19001142 Free PMC article.
Molecular dynamics simulations of membrane channels and transporters.
Khalili-Araghi F, Gumbart J, Wen PC, Sotomayor M, Tajkhorshid E, Schulten K. Khalili-Araghi F, et al. Among authors: gumbart j. Curr Opin Struct Biol. 2009 Apr;19(2):128-37. doi: 10.1016/j.sbi.2009.02.011. Epub 2009 Apr 1. Curr Opin Struct Biol. 2009. PMID: 19345092 Free PMC article. Review.
Protein-induced membrane curvature investigated through molecular dynamics flexible fitting.
Hsin J, Gumbart J, Trabuco LG, Villa E, Qian P, Hunter CN, Schulten K. Hsin J, et al. Among authors: gumbart j. Biophys J. 2009 Jul 8;97(1):321-9. doi: 10.1016/j.bpj.2009.04.031. Biophys J. 2009. PMID: 19580770 Free PMC article.
Coupling of calcium and substrate binding through loop alignment in the outer-membrane transporter BtuB.
Gumbart J, Wiener MC, Tajkhorshid E. Gumbart J, et al. J Mol Biol. 2009 Nov 13;393(5):1129-42. doi: 10.1016/j.jmb.2009.09.004. Epub 2009 Sep 9. J Mol Biol. 2009. PMID: 19747487 Free PMC article.
Regulation of the protein-conducting channel by a bound ribosome.
Gumbart J, Trabuco LG, Schreiner E, Villa E, Schulten K. Gumbart J, et al. Structure. 2009 Nov 11;17(11):1453-64. doi: 10.1016/j.str.2009.09.010. Structure. 2009. PMID: 19913480 Free PMC article.
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