James C. Gumbart, Ph.D. - Publications

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

112 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
2022 Fu H, Chen H, Blazhynska M, Goulard Coderc de Lacam E, Szczepaniak F, Pavlova A, Shao X, Gumbart JC, Dehez F, Roux B, Cai W, Chipot C. Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations. Nature Protocols. PMID 35277695 DOI: 10.1038/s41596-021-00676-1  0.443
2022 Acharya A, Yi D, Pavlova A, Agarwal V, Gumbart JC. Resolving the Hydride Transfer Pathway in Oxidative Conversion of Proline to Pyrrole. Biochemistry. PMID 35072459 DOI: 10.1021/acs.biochem.1c00741  0.569
2021 Akey CW, Singh D, Ouch C, Echeverria I, Nudelman I, Varberg JM, Yu Z, Fang F, Shi Y, Wang J, Salzberg D, Song K, Xu C, Gumbart JC, Suslov S, et al. Comprehensive structure and functional adaptations of the yeast nuclear pore complex. Cell. PMID 34982960 DOI: 10.1016/j.cell.2021.12.015  0.504
2021 Wu R, Bakelar JW, Lundquist K, Zhang Z, Kuo KM, Ryoo D, Pang YT, Sun C, White T, Klose T, Jiang W, Gumbart JC, Noinaj N. Plasticity within the barrel domain of BamA mediates a hybrid-barrel mechanism by BAM. Nature Communications. 12: 7131. PMID 34880256 DOI: 10.1038/s41467-021-27449-4  0.347
2021 Gumbart JC, Ferreira JL, Hwang H, Hazel AJ, Cooper CJ, Parks JM, Smith JC, Zgurskaya HI, Beeby M. Lpp positions peptidoglycan at the AcrA-TolC interface in the AcrAB-TolC multidrug efflux pump. Biophysical Journal. PMID 34411576 DOI: 10.1016/j.bpj.2021.08.016  0.51
2021 Zhan Z, Ryoo D, Balusek C, Acharya A, Rydmark MO, Linke D, Gumbart JC. Inward-facing glycine residues create sharp turns in β-barrel membrane proteins. Biochimica Et Biophysica Acta. Biomembranes. 183662. PMID 34097860 DOI: 10.1016/j.bbamem.2021.183662  0.571
2021 Pavlova A, Zhang Z, Acharya A, Lynch DL, Pang YT, Mou Z, Parks JM, Chipot C, Gumbart JC. Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. The Journal of Physical Chemistry Letters. 5494-5502. PMID 34086459 DOI: 10.1021/acs.jpclett.1c01494  0.58
2021 Acharya A, Lynch DL, Pavlova A, Pang YT, Gumbart JC. ACE2 glycans preferentially interact with SARS-CoV-2 over SARS-CoV. Chemical Communications (Cambridge, England). PMID 34019602 DOI: 10.1039/d1cc02305e  0.524
2021 Yi D, Acharya A, Gumbart JC, Gutekunst WR, Agarwal V. Gatekeeping Ketosynthases Dictate Initiation of Assembly Line Biosynthesis of Pyrrolic Polyketides. Journal of the American Chemical Society. PMID 33989500 DOI: 10.1021/jacs.1c02371  0.534
2021 Zanetti-Polzi L, Smith MD, Chipot C, Gumbart JC, Lynch DL, Pavlova A, Smith JC, Daidone I. Tuning Proton Transfer Thermodynamics in SARS-CoV-2 Main Protease: Implications for Catalysis and Inhibitor Design. The Journal of Physical Chemistry Letters. 4195-4202. PMID 33900080 DOI: 10.1021/acs.jpclett.1c00425  0.355
2021 Li Y, Liu J, Gumbart JC. Preparing Membrane Proteins for Simulation Using CHARMM-GUI. Methods in Molecular Biology (Clifton, N.J.). 2302: 237-251. PMID 33877631 DOI: 10.1007/978-1-0716-1394-8_13  0.392
2020 Pavlova A, Lynch DL, Daidone I, Zanetti-Polzi L, Smith MD, Chipot C, Kneller DW, Kovalevsky A, Coates L, Golosov AA, Dickson CJ, Velez-Vega C, Duca JS, Vermaas JV, Pang YT, ... ... Gumbart JC, et al. Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease. Chemical Science. 12: 1513-1527. PMID 35356437 DOI: 10.1039/d0sc04942e  0.627
2020 Acharya A, Agarwal R, Baker M, Baudry J, Bhowmik D, Boehm S, Byler K, Coates L, Chen SY, Cooper CJ, Demerdash O, Daidone I, Eblen J, Ellingson SR, Forli S, ... ... Gumbart JC, et al. Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. Chemrxiv : the Preprint Server For Chemistry. PMID 33200117 DOI: 10.26434/chemrxiv.12725465.v1  0.627
2020 Zanetti-Polzi L, Smith M, Chipot C, Gumbart JC, Lynch DL, Pavlova A, Smith JC, Daidone I. Tuning Proton Transfer Thermodynamics in SARS-Cov-2 Main Protease: Implications for Catalysis and Inhibitor Design. Chemrxiv : the Preprint Server For Chemistry. PMID 33200115 DOI: 10.26434/chemrxiv.13200227  0.359
2020 Liu J, Gumbart JC. Membrane thinning and lateral gating are consistent features of BamA across multiple species. Plos Computational Biology. 16: e1008355. PMID 33112853 DOI: 10.1371/journal.pcbi.1008355  0.345
2020 Pavlova A, Lynch DL, Daidone I, Zanetti-Polzi L, Smith MD, Chipot C, Kneller DW, Kovalevsky A, Coates L, Golosov AA, Dickson CJ, Velez-Vega C, Duca JS, Vermaas JV, Pang YT, ... ... Gumbart JC, et al. Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease. Biorxiv : the Preprint Server For Biology. PMID 32935106 DOI: 10.1101/2020.09.07.286344  0.627
2020 Acharya A, Stockmann J, Beyer L, Rudack T, Nabers A, Gumbart JC, Gerwert K, Batista VS. The Effect of (-)-Epigallocatechin-3-Gallate on the Amyloid-β Secondary Structure. Biophysical Journal. PMID 32579965 DOI: 10.1016/J.Bpj.2020.05.033  0.675
2020 Heinrich F, Salyapongse A, Kumagai A, Dupuy FG, Shukla K, Penk A, Huster D, Ernst RK, Pavlova A, Gumbart JC, Deslouches B, Di YP, Tristram-Nagle S. Synergistic Biophysical Techniques Reveal Structural Mechanisms of Engineered Cationic Antimicrobial Peptides in Lipid Model Membranes. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 32166806 DOI: 10.1002/Chem.202000212  0.393
2020 Ryoo D, Rydmark MO, Pang YT, Lundquist KP, Linke D, Gumbart JC. BamA is required for autotransporter secretion. Biochimica Et Biophysica Acta. General Subjects. 129581. PMID 32114025 DOI: 10.1016/J.Bbagen.2020.129581  0.331
2020 Domínguez-Medina CC, Pérez-Toledo M, Schager AE, Marshall JL, Cook CN, Bobat S, Hwang H, Chun BJ, Logan E, Bryant JA, Channell WM, Morris FC, Jossi SE, Alshayea A, Rossiter AE, ... ... Gumbart JC, et al. Outer membrane protein size and LPS O-antigen define protective antibody targeting to the Salmonella surface. Nature Communications. 11: 851. PMID 32051408 DOI: 10.1038/S41467-020-14655-9  0.612
2020 Acharya A, Stockmann J, Beyer L, Nabers A, Gerwert K, Gumbart JC, Batista VS. The Effect of (-)-Epigallocatechin-3-Gallate on the Aβ Secondary Structure Biophysical Journal. 118: 47a. DOI: 10.1016/J.Bpj.2019.11.437  0.643
2020 Gumbart JC, Ferreira J, hwang S, Hazel A, Parks JM, Smith JC, Beeby M, Zgurskaya H. Modeling the Placement of the AcrAB-TolC Multidrug Efflux Pump in the Bacterial Cell Envelope Biophysical Journal. 118: 13a. DOI: 10.1016/J.Bpj.2019.11.251  0.416
2020 Pavlova A, Gumbart JC. Mechanism of Action of HBV Capsid Assembly Modulators can be Predicted from a Combination of Molecular Dynamics and Docking Biophysical Journal. 118: 179a. DOI: 10.1016/J.Bpj.2019.11.1095  0.306
2019 Hwang H, Hazel A, Lian P, Smith JC, Gumbart JC, Parks JM. A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins. Journal of Computational Chemistry. PMID 31721253 DOI: 10.1002/Jcc.26098  0.584
2019 Hazel A, Abdali N, Leus I, Parks JM, Smith JC, Zgurskaya HI, Gumbart JC. Conformational dynamics of AcrA govern multidrug efflux pump assembly. Acs Infectious Diseases. PMID 31517484 DOI: 10.1021/Acsinfecdis.9B00273  0.582
2019 Lundquist KP, Gumbart JC. Presence of substrate aids lateral gate separation in LptD. Biochimica Et Biophysica Acta. Biomembranes. PMID 31351059 DOI: 10.1016/J.Bbamem.2019.07.013  0.436
2019 Hill SE, Kwon MS, Martin MD, Suntharalingam A, Hazel A, Dickey CA, Gumbart JC, Lieberman RL. Stable calcium-free myocilin olfactomedin domain variants reveal challenges in differentiating between benign and glaucoma-causing mutations. The Journal of Biological Chemistry. PMID 31270212 DOI: 10.1074/Jbc.Ra119.009419  0.342
2019 Balusek C, Hwang H, Lau CH, Lundquist K, Hazel A, Pavlova A, Lynch DL, Reggio PH, Wang Y, Gumbart JC. Accelerating Membrane Simulations with Hydrogen Mass Repartitioning. Journal of Chemical Theory and Computation. PMID 31265271 DOI: 10.1021/Acs.Jctc.9B00160  0.442
2019 Strickland KM, Stock G, Cui G, Hwang H, Infield DT, Schmidt-Krey I, McCarty NA, Gumbart JC. ATP-Dependent Signaling in Simulations of a Revised Model of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR). The Journal of Physical Chemistry. B. PMID 30921517 DOI: 10.1021/Acs.Jpcb.8B11970  0.35
2019 Darzynkiewicz ZM, Green AT, Abdali N, Hazel A, Fulton RL, Kimball J, Gryczynski Z, Gumbart JC, Parks JM, Smith JC, Zgurskaya HI. Identification of Binding Sites for Efflux Pump Inhibitors of the AcrAB-TolC Component AcrA. Biophysical Journal. PMID 30691677 DOI: 10.1016/J.Bpj.2019.01.010  0.459
2019 Brady NG, Li M, Ma Y, Gumbart JC, Bruce BD. Non-detergent isolation of a cyanobacterial photosystem I using styrene maleic acid alternating copolymers Rsc Advances. 9: 31781-31796. DOI: 10.1039/C9Ra04619D  0.385
2019 Gumbart JC, Balusek C, Hwang H, Hon Lau C, Lundquist K, Hazel A, Pavlova A, Lynch D, Reggio P, Wang Y. On the Validity of Hydrogen Mass Repartitioning for CHARMM36 Membrane Systems in NAMD Biophysical Journal. 116: 141a. DOI: 10.1016/J.Bpj.2018.11.782  0.334
2018 Bañó-Polo M, Baeza-Delgado C, Tamborero S, Hazel A, Grau B, Nilsson I, Whitley P, Gumbart JC, von Heijne G, Mingarro I. Transmembrane but not soluble helices fold inside the ribosome tunnel. Nature Communications. 9: 5246. PMID 30531789 DOI: 10.1038/S41467-018-07554-7  0.436
2018 Hwang H, Paracini N, Parks JM, Lakey JH, Gumbart JC. Distribution of mechanical stress in the Escherichia coli cell envelope. Biochimica Et Biophysica Acta. Biomembranes. PMID 30278180 DOI: 10.1016/j.bbamem.2018.09.020  0.358
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  0.68
2018 Lundquist K, Bakelar J, Noinaj N, Gumbart JC. C-terminal kink formation is required for lateral gating in BamA. Proceedings of the National Academy of Sciences of the United States of America. PMID 30087180 DOI: 10.1073/Pnas.1722530115  0.425
2018 Gumbart JC, Ulmschneider MB, Hazel A, White SH, Ulmschneider JP. Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method. The Journal of Membrane Biology. PMID 29520628 DOI: 10.1007/S00232-018-0026-Y  0.379
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  0.334
2018 Pavlova A, Parks JM, Gumbart JC. Development of CHARMM-compatible force-field parameters for cobalamin and related cofactors from quantum mechanical calculations. Journal of Chemical Theory and Computation. PMID 29334459 DOI: 10.1021/Acs.Jctc.7B01236  0.346
2018 Hazel A, Rowley C, Gumbart JC. Molecular Dynamics Investigations of β-Sheet Stability and Folding Pathways Biophysical Journal. 114: 54a. DOI: 10.1016/J.Bpj.2017.11.346  0.63
2017 Hill SE, Nguyen E, Donegan RK, Patterson-Orazem AC, Hazel A, Gumbart JC, Lieberman RL. Structure and Misfolding of the Flexible Tripartite Coiled-Coil Domain of Glaucoma-Associated Myocilin. Structure (London, England : 1993). PMID 29056483 DOI: 10.1016/J.Str.2017.09.008  0.351
2017 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. Structural basis for substrate selection by the translocation and assembly module of the beta-barrel assembly machinery. Molecular Microbiology. PMID 28752534 DOI: 10.1111/Mmi.13757  0.417
2017 Pavlova A, Parks JM, Oyelere AK, Gumbart JC. Toward the rational design of macrolide antibiotics to combat resistance. Chemical Biology & Drug Design. PMID 28419786 DOI: 10.1111/Cbdd.13004  0.307
2017 Hwang H, McCaslin TG, Hazel A, Pagba CV, Nevin CM, Pavlova A, Barry BA, Gumbart JC. Redox-Driven Conformational Dynamics in a Photosystem-II-Inspired β-Hairpin Maquette Determined through Spectroscopy and Simulation. The Journal of Physical Chemistry. B. PMID 28145121 DOI: 10.1021/Acs.Jpcb.6B09481  0.336
2017 Lundquist K, Gumbart JC. Simulations of Bama in a Native Outer-Membrane Model and Energetics of Lateral Opening Biophysical Journal. 112: 504a. DOI: 10.1016/J.Bpj.2016.11.2728  0.461
2017 Pavlova A, Parks JM, Oyelere AK, Gumbart JC. Towards a Rational Design of Macrolide Antibiotics in Order to Combat Bacterial Resistance Biophysical Journal. 112: 323a. DOI: 10.1016/J.Bpj.2016.11.1749  0.316
2016 Deeng J, Chan KY, van der Sluis EO, Berninghausen O, Han W, Gumbart J, Schulten K, Beatrix B, Beckmann R. Dynamic behavior of trigger factor on the ribosome. Journal of Molecular Biology. PMID 27320387 DOI: 10.1016/J.Jmb.2016.06.007  0.517
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  0.346
2016 Gumbart JC, Noskov S. Membrane proteins: Where theory meets experiment. Biochimica Et Biophysica Acta. PMID 27094366 DOI: 10.1016/J.Bbamem.2016.04.007  0.585
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  0.681
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  0.483
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  0.479
2016 Lundquist K, Herndon C, Harty TH, Gumbart JC. Accelerating the use of molecular modeling in the high school classroom with VMD Lite. Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology. PMID 26751137 DOI: 10.1002/Bmb.20940  0.338
2016 Stock G, McCarty N, Gumbart JC. Refinement of a Recent CFTR Homology Model Guided by Pore Formation Biophysical Journal. 110: 140a-141a. DOI: 10.1016/J.Bpj.2015.11.799  0.42
2016 Nguyen LT, Swulius M, Gumbart JC, Beeby M, Jensen GJ. Coarse-Grained Simulations Reveal Mechanisms of Bacterial Morphogenesis Biophysical Journal. 110: 468a. DOI: 10.1016/J.Bpj.2015.11.2505  0.322
2016 Lundquist K, Mayclin SJ, Buchanan SK, Gumbart JC. Structure and Dynamics of the LPS Insertase LptD/E in a Realistic Outer-Membrane Model Biophysical Journal. 110: 383a-384a. DOI: 10.1016/J.Bpj.2015.11.2072  0.416
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  0.322
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  0.309
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  0.425
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  0.385
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  0.31
2015 Stock G, Cui G, McCarty NA, Gumbart JC. Refinement and Evaluation of a CFTR Homology Model and Identification of Residues Controlling Channel Gating Biophysical Journal. 108: 127a. DOI: 10.1016/J.Bpj.2014.11.708  0.383
2015 Lundquist K, Gumbart JC. Insertion of β-Barrel Proteins in Gram-Negative Bacteria Biophysical Journal. 108: 364a. DOI: 10.1016/J.Bpj.2014.11.1994  0.469
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  0.452
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  0.662
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  0.513
2014 Park E, Ménétret JF, Gumbart JC, Ludtke SJ, Li W, Whynot A, Rapoport TA, Akey CW. Structure of the SecY channel during initiation of protein translocation. Nature. 506: 102-6. PMID 24153188 DOI: 10.1038/Nature12720  0.361
2014 Balusek C, Gumbart JC. Comparing Symmetric and Asymmetric Bilayer-Protein Interactions using Molecular Dynamics Biophysical Journal. 106: 100a. DOI: 10.1016/J.Bpj.2013.11.623  0.469
2014 Pavlova A, Gumbart JC. Resolving the Mechanisms of Bacterial Resistance to Macrolide Antibiotics Biophysical Journal. 106: 39a. DOI: 10.1016/J.Bpj.2013.11.289  0.323
2014 Jiang W, Phillips J, Huang L, Fajer M, Meng Y, Gumbart JC, luo y, Schulten K, roux b. Generalized Scalable Multiple Copy Algorithms for Biological Molecular Dynamics Simulations in NAMD Biophysical Journal. 106: 412a. DOI: 10.1016/J.Bpj.2013.11.2316  0.664
2014 Gumbart JC. Mechanisms of Membrane-Protein Insertion at the Inner and Outer Membranes Biophysical Journal. 106: 267a. DOI: 10.1016/J.Bpj.2013.11.1563  0.492
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  0.537
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  0.787
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  0.473
2013 Farelli JD, Gumbart JC, Akey IV, Hempstead A, Amyot W, Head JF, McKnight CJ, Isberg RR, Akey CW. IcmQ in the Type 4b secretion system contains an NAD+ binding domain. Structure (London, England : 1993). 21: 1361-73. PMID 23850453 DOI: 10.1016/J.Str.2013.05.017  0.357
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  0.492
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  0.466
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: 10.1016/J.Bpj.2012.11.2274  0.679
2013 Gumbart JC, Beeby M, Jensen G, Roux B. Assembly and Architecture of Gram-Positive and -Negative Cell Walls Biophysical Journal. 104: 642a. DOI: 10.1016/J.Bpj.2012.11.3544  0.51
2013 Mayne CG, Gumbart JC, Tajkhorshid E. The Force Field Toolkit: Software for the Parameterization of Small Molecules from First Principles Biophysical Journal. 104: 31a. DOI: 10.1016/J.Bpj.2012.11.209  0.329
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  0.511
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  0.594
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  0.324
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  0.386
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  0.812
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  0.778
2012 Gumbart JC, Roux B, Schulten K. Spontaneous Movement of Transmembrane Segments from SecY into the Membrane Biophysical Journal. 102: 431a. DOI: 10.1016/J.Bpj.2011.11.2359  0.665
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  0.485
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  0.568
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  0.598
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  0.582
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  0.795
2011 Beckmann R, Frauenfeld J, Gumbart J, Schulten K. Cryo-EM of the ribosome–SecYEG complex in nanodiscs Acta Crystallographica Section a Foundations of Crystallography. 67: C24-C25. DOI: 10.1107/S0108767311099521  0.43
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  0.714
2011 Gumbart JC, Chipot C, Schulten K. Protein Folding and Membrane Insertion via the Protein Translocon Biophysical Journal. 100: 203a. DOI: 10.1016/J.Bpj.2010.12.1322  0.573
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  0.734
2010 Gumbart JC, Chipot C, Schulten K. The Role of the Protein-Conducting Channel in the Membrane Insertion of Transmembrane Segments Biophysical Journal. 98: 224a. DOI: 10.1016/J.Bpj.2009.12.1213  0.585
2010 Chan KY, Trabuco LG, Gumbart J, Schulten K. Recent Developments of the Molecular Dynamics Flexible Fitting Method Biophysical Journal. 98: 11a. DOI: 10.1016/J.Bpj.2009.12.065  0.768
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  0.728
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  0.528
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  0.793
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  0.347
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  0.81
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  0.797
2009 Gumbart JC, Wiener MC, Tajkhorshid E. Coupling of Ca2+ and Substrate Binding in the Outer Membrane Transporter BtuB Biophysical Journal. 96: 272a. DOI: 10.1016/J.Bpj.2008.12.1346  0.32
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 DOI: 10.1085/Jgp.200810062  0.538
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  0.745
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  0.569
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  0.41
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  0.553
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  0.746
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  0.621
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