James C. Gumbart, Ph.D. - Publications

Affiliations: 
2013- Physics Georgia Institute of Technology, Atlanta, GA 

55 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Hazel AJ, Walters ET, Rowley CN, Gumbart JC. Folding free energy landscapes of -sheets with non-polarizable and polarizable CHARMM force fields. The Journal of Chemical Physics. 149: 072317. PMID 30134731 DOI: 10.1063/1.5025951  0.52
2018 Fu H, Gumbart JC, Chen H, Shao X, Cai W, Chipot C. BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-energy Calculations. Journal of Chemical Information and Modeling. PMID 29405709 DOI: 10.1021/acs.jcim.7b00695  0.52
2016 Nguyen LT, Gumbart JC, Jensen GJ. Coarse-Grained Molecular Dynamics Simulations of the Bacterial Cell Wall. Methods in Molecular Biology (Clifton, N.J.). 1440: 247-70. PMID 27311677 DOI: 10.1007/978-1-4939-3676-2_18  0.64
2016 Waters JT, Kim HD, Gumbart JC, Lu XJ, Harvey SC. DNA Scrunching in the Packaging of Viral Genomes. The Journal of Physical Chemistry. B. PMID 27214211 DOI: 10.1021/acs.jpcb.6b02149  0.64
2016 Botos I, Majdalani N, Mayclin SJ, McCarthy JG, Lundquist K, Wojtowicz D, Barnard TJ, Gumbart JC, Buchanan SK. Structural and Functional Characterization of the LPS Transporter LptDE from Gram-Negative Pathogens. Structure (London, England : 1993). PMID 27161977 DOI: 10.1016/j.str.2016.03.026  0.64
2016 Waters JT, Lu XJ, Galindo-Murillo R, Gumbart JC, Kim HD, Cheatham TE, Harvey SC. Transitions of Double-Stranded DNA Between the A- and B-Forms. The Journal of Physical Chemistry. B. PMID 27135262 DOI: 10.1021/acs.jpcb.6b02155  0.64
2016 Lee CT, Comer J, Herndon C, Leung N, Pavlova A, Swift RV, Tung C, Rowley C, Amaro RE, Chipot C, Wang Y, Gumbart JC. Simulation-based approaches for determining membrane permeability of small compounds. Journal of Chemical Information and Modeling. PMID 27043429 DOI: 10.1021/acs.jcim.6b00022  0.64
2016 Gumbart JC, Chipot C. Decrypting protein insertion through the translocon with free-energy calculations. Biochimica Et Biophysica Acta. PMID 26896694 DOI: 10.1016/j.bbamem.2016.02.017  0.64
2016 Pavlova A, Hwang H, Lundquist K, Balusek C, Gumbart JC. Living on the edge: Simulations of bacterial outer-membrane proteins. Biochimica Et Biophysica Acta. PMID 26826270 DOI: 10.1016/j.bbamem.2016.01.020  0.64
2015 Pavlova A, Gumbart JC. Parametrization of macrolide antibiotics using the force field toolkit. Journal of Computational Chemistry. 36: 2052-63. PMID 26280362 DOI: 10.1002/jcc.24043  0.64
2015 Nguyen LT, Gumbart JC, Beeby M, Jensen GJ. Coarse-grained simulations of bacterial cell wall growth reveal that local coordination alone can be sufficient to maintain rod shape. Proceedings of the National Academy of Sciences of the United States of America. PMID 26130803 DOI: 10.1073/pnas.1504281112  0.64
2015 Chen Y, Bauer BW, Rapoport TA, Gumbart JC. Conformational Changes of the Clamp of the Protein Translocation ATPase SecA. Journal of Molecular Biology. 427: 2348-59. PMID 25982945 DOI: 10.1016/j.jmb.2015.05.003  0.64
2015 Johnson JL, Entzminger KC, Hyun J, Kalyoncu S, Heaner DP, Morales IA, Sheppard A, Gumbart JC, Maynard JA, Lieberman RL. Structural and biophysical characterization of an epitope-specific engineered Fab fragment and complexation with membrane proteins: implications for co-crystallization. Acta Crystallographica. Section D, Biological Crystallography. 71: 896-906. PMID 25849400 DOI: 10.1107/S1399004715001856  0.64
2015 Comer J, Gumbart JC, Hénin J, Lelièvre T, Pohorille A, Chipot C. The adaptive biasing force method: everything you always wanted to know but were afraid to ask. The Journal of Physical Chemistry. B. 119: 1129-51. PMID 25247823 DOI: 10.1021/jp506633n  0.64
2014 Hazel A, Chipot C, Gumbart JC. Thermodynamics of Deca-alanine Folding in Water. Journal of Chemical Theory and Computation. 10: 2836-2844. PMID 25061447 DOI: 10.1021/ct5002076  0.64
2014 Noinaj N, Kuszak AJ, Balusek C, Gumbart JC, Buchanan SK. Lateral opening and exit pore formation are required for BamA function. Structure (London, England : 1993). 22: 1055-62. PMID 24980798 DOI: 10.1016/j.str.2014.05.008  0.64
2014 Jiang W, Phillips JC, Huang L, Fajer M, Meng Y, Gumbart JC, Luo Y, Schulten K, Roux B. Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD. Computer Physics Communications. 185: 908-916. PMID 24944348 DOI: 10.1016/j.cpc.2013.12.014  0.64
2014 Gumbart JC, Beeby M, Jensen GJ, Roux B. Escherichia coli peptidoglycan structure and mechanics as predicted by atomic-scale simulations. Plos Computational Biology. 10: e1003475. PMID 24586129 DOI: 10.1371/journal.pcbi.1003475  0.64
2013 Gumbart JC, Roux B, Chipot C. Efficient determination of protein-protein standard binding free energies from first principles. Journal of Chemical Theory and Computation. 9. PMID 24179453 DOI: 10.1021/ct400273t  0.64
2013 Khalili-Araghi F, Ziervogel B, Gumbart JC, Roux B. Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations. The Journal of General Physiology. 142: 465-75. PMID 24081985 DOI: 10.1085/jgp.201311014  0.64
2013 Mayne CG, Saam J, Schulten K, Tajkhorshid E, Gumbart JC. Rapid parameterization of small molecules using the Force Field Toolkit. Journal of Computational Chemistry. 34: 2757-70. PMID 24000174 DOI: 10.1002/jcc.23422  0.64
2013 Noinaj N, Kuszak AJ, Gumbart JC, Lukacik P, Chang H, Easley NC, Lithgow T, Buchanan SK. Structural insight into the biogenesis of β-barrel membrane proteins. Nature. 501: 385-90. PMID 23995689 DOI: 10.1038/nature12521  0.64
2013 Weber BW, Kimani SW, Varsani A, Cowan DA, Hunter R, Venter GA, Gumbart JC, Sewell BT. The mechanism of the amidases: mutating the glutamate adjacent to the catalytic triad inactivates the enzyme due to substrate mispositioning. The Journal of Biological Chemistry. 288: 28514-23. PMID 23946488 DOI: 10.1074/jbc.M113.503284  0.64
2013 Briegel A, Ames P, Gumbart JC, Oikonomou CM, Parkinson JS, Jensen GJ. The mobility of two kinase domains in the Escherichia coli chemoreceptor array varies with signalling state. Molecular Microbiology. 89: 831-41. PMID 23802570 DOI: 10.1111/mmi.12309  0.64
2013 Gumbart JC, Roux B, Chipot C. Standard binding free energies from computer simulations: What is the best strategy? Journal of Chemical Theory and Computation. 9: 794-802. PMID 23794960 DOI: 10.1021/ct3008099  0.64
2013 Beeby M, Gumbart JC, Roux B, Jensen GJ. Architecture and assembly of the Gram-positive cell wall. Molecular Microbiology. 88: 664-72. PMID 23600697 DOI: 10.1111/mmi.12203  0.64
2013 Gumbart JC, Teo I, Roux B, Schulten K. Reconciling the roles of kinetic and thermodynamic factors in membrane-protein insertion. Journal of the American Chemical Society. 135: 2291-7. PMID 23298280 DOI: 10.1021/ja310777k  0.64
2012 Broadley SG, Gumbart JC, Weber BW, Marakalala MJ, Steenkamp DJ, Sewell BT. A new crystal form of MshB from Mycobacterium tuberculosis with glycerol and acetate in the active site suggests the catalytic mechanism. Acta Crystallographica. Section D, Biological Crystallography. 68: 1450-9. PMID 23090394 DOI: 10.1107/S090744491203449X  0.64
2012 Gumbart J. Exploring substrate diffusion in channels using biased molecular dynamics simulations Methods in Molecular Biology (Clifton, N.J.). 914: 337-350. PMID 22976037 DOI: 10.1007/978-1-62703-23-6_19  0.64
2012 Gumbart J, Schreiner E, Wilson DN, Beckmann R, Schulten K. Mechanisms of SecM-mediated stalling in the ribosome. Biophysical Journal. 103: 331-41. PMID 22853911 DOI: 10.1016/j.bpj.2012.06.005  0.64
2012 Gumbart J, Roux B. Determination of membrane-insertion free energies by molecular dynamics simulations. Biophysical Journal. 102: 795-801. PMID 22385850 DOI: 10.1016/j.bpj.2012.01.021  0.64
2012 Noinaj N, Easley NC, Oke M, Mizuno N, Gumbart J, Boura E, Steere AN, Zak O, Aisen P, Tajkhorshid E, Evans RW, Gorringe AR, Mason AB, Steven AC, Buchanan SK. Structural basis for iron piracy by pathogenic Neisseria. Nature. 483: 53-8. PMID 22327295 DOI: 10.1038/nature10823  0.64
2012 Barnard TJ, Gumbart J, Peterson JH, Noinaj N, Easley NC, Dautin N, Kuszak AJ, Tajkhorshid E, Bernstein HD, Buchanan SK. Molecular basis for the activation of a catalytic asparagine residue in a self-cleaving bacterial autotransporter. Journal of Molecular Biology. 415: 128-42. PMID 22094314 DOI: 10.1016/j.jmb.2011.10.049  0.64
2012 Gumbart J, Khalili-Araghi F, Sotomayor M, Roux B. Constant electric field simulations of the membrane potential illustrated with simple systems. Biochimica Et Biophysica Acta. 1818: 294-302. PMID 22001851 DOI: 10.1016/j.bbamem.2011.09.030  0.64
2012 Khalili-Araghi F, Ziervogel B, Roux B, Gumbart J. Membrane protein simulations under asymmetric ionic concentrations Acm International Conference Proceeding Series. DOI: 10.1145/2335755.2335812  0.64
2011 Chan KY, Gumbart J, McGreevy R, Watermeyer JM, Sewell BT, Schulten K. Symmetry-restrained flexible fitting for symmetric EM maps. Structure (London, England : 1993). 19: 1211-8. PMID 21893283 DOI: 10.1016/j.str.2011.07.017  0.64
2011 Gumbart J, Chipot C, Schulten K. Free energy of nascent-chain folding in the translocon. Journal of the American Chemical Society. 133: 7602-7. PMID 21524073 DOI: 10.1021/ja2019299  0.64
2011 Frauenfeld J, Gumbart J, Sluis EO, Funes S, Gartmann M, Beatrix B, Mielke T, Berninghausen O, Becker T, Schulten K, Beckmann R. Cryo-EM structure of the ribosome-SecYE complex in the membrane environment. Nature Structural & Molecular Biology. 18: 614-21. PMID 21499241 DOI: 10.1038/nsmb.2026  0.64
2011 Gumbart J, Chipot C, Schulten K. Free-energy cost for translocon-assisted insertion of membrane proteins. Proceedings of the National Academy of Sciences of the United States of America. 108: 3596-601. PMID 21317362 DOI: 10.1073/pnas.1012758108  0.64
2011 Trabuco LG, Schreiner E, Gumbart J, Hsin J, Villa E, Schulten K. Applications of the molecular dynamics flexible fitting method. Journal of Structural Biology. 173: 420-7. PMID 20932910 DOI: 10.1016/j.jsb.2010.09.024  0.64
2011 Gumbart J, Schreiner E, Trabuco LG, Chan KY, Schulten K. Viewing the mechanisms of translation through the computational microscope Molecular Machines in Biology: Workshop of the Cell. 142-157. DOI: 10.1017/CBO9781139003704.010  0.64
2010 Hsin J, Chandler DE, Gumbart J, Harrison CB, Sener M, Strumpfer J, Schulten K. Self-assembly of photosynthetic membranes. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 11: 1154-9. PMID 20183845 DOI: 10.1002/cphc.200900911  0.64
2009 Chandler DE, Gumbart J, Stack JD, Chipot C, Schulten K. Membrane curvature induced by aggregates of LH2s and monomeric LH1s. Biophysical Journal. 97: 2978-84. PMID 19948127 DOI: 10.1016/j.bpj.2009.09.007  0.64
2009 Becker T, Bhushan S, Jarasch A, Armache JP, Funes S, Jossinet F, Gumbart J, Mielke T, Berninghausen O, Schulten K, Westhof E, Gilmore R, Mandon EC, Beckmann R. Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome. Science (New York, N.Y.). 326: 1369-73. PMID 19933108 DOI: 10.1126/science.1178535  0.64
2009 Gumbart J, Trabuco LG, Schreiner E, Villa E, Schulten K. Regulation of the protein-conducting channel by a bound ribosome. Structure (London, England : 1993). 17: 1453-64. PMID 19913480 DOI: 10.1016/j.str.2009.09.010  0.64
2009 Gumbart J, Wiener MC, Tajkhorshid E. Coupling of calcium and substrate binding through loop alignment in the outer-membrane transporter BtuB. Journal of Molecular Biology. 393: 1129-42. PMID 19747487 DOI: 10.1016/j.jmb.2009.09.004  0.64
2009 Hsin J, Gumbart J, Trabuco LG, Villa E, Qian P, Hunter CN, Schulten K. Protein-induced membrane curvature investigated through molecular dynamics flexible fitting. Biophysical Journal. 97: 321-9. PMID 19580770 DOI: 10.1016/j.bpj.2009.04.031  0.64
2009 Khalili-Araghi F, Gumbart J, Wen PC, Sotomayor M, Tajkhorshid E, Schulten K. Molecular dynamics simulations of membrane channels and transporters. Current Opinion in Structural Biology. 19: 128-37. PMID 19345092 DOI: 10.1016/j.sbi.2009.02.011  0.64
2008 Gumbart J, Schulten K. The roles of pore ring and plug in the secY protein-conducting channel Journal of General Physiology. 132: 709-719. PMID 19001142  0.64
2008 Chandler DE, Hsin J, Harrison CB, Gumbart J, Schulten K. Intrinsic curvature properties of photosynthetic proteins in chromatophores. Biophysical Journal. 95: 2822-36. PMID 18515401 DOI: 10.1529/biophysj.108.132852  0.64
2007 Gumbart J, Schulten K. Structural determinants of lateral gate opening in the protein translocon Biochemistry. 46: 11147-11157. PMID 17760424 DOI: 10.1021/bi700835d  0.64
2007 Gumbart J, Wiener MC, Tajkhorshid E. Mechanics of force propagation in TonB-dependent outer membrane transport. Biophysical Journal. 93: 496-504. PMID 17449669 DOI: 10.1529/biophysj.107.104158  0.64
2006 Gumbart J, Schulten K. Molecular dynamics studies of the archaeal translocon Biophysical Journal. 90: 2356-2367. PMID 16415058 DOI: 10.1529/biophysj.105.075291  0.64
2005 Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry. 26: 1781-802. PMID 16222654 DOI: 10.1002/jcc.20289  0.64
2005 Gumbart J, Wang Y, Aksimentiev A, Tajkhorshid E, Schulten K. Molecular dynamics simulations of proteins in lipid bilayers Current Opinion in Structural Biology. 15: 423-431. PMID 16043343 DOI: 10.1016/j.sbi.2005.07.007  0.64
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