| Year |
Citation |
Score |
| 2024 |
Wu K, Itskanov S, Lynch DL, Chen Y, Turner A, Gumbart JC, Park E. Substrate recognition mechanism of the endoplasmic reticulum-associated ubiquitin ligase Doa10. Biorxiv : the Preprint Server For Biology. PMID 38260251 DOI: 10.1101/2024.01.09.574907 |
0.32 |
|
| 2023 |
Blazhynska M, Gumbart JC, Chen H, Tajkhorshid E, Roux B, Chipot C. A Rigorous Framework for Calculating Protein-Protein Binding Affinities in Membranes. Journal of Chemical Theory and Computation. 19: 9077-9092. PMID 38091976 DOI: 10.1021/acs.jctc.3c00941 |
0.527 |
|
| 2023 |
Lui VG, Hoenig M, Cabrera-Martinez B, Baxter RM, Garcia-Perez JE, Bailey O, Acharya A, Lundquist K, Capera J, Matusewicz P, Hartl FA, D'Abramo M, Alba J, Jacobsen EM, Niewolik D, ... ... Gumbart JC, et al. A partial human LCK defect causes a T cell immunodeficiency with intestinal inflammation. The Journal of Experimental Medicine. 221. PMID 37962568 DOI: 10.1084/jem.20230927 |
0.486 |
|
| 2023 |
Sim SI, Chen Y, Lynch DL, Gumbart JC, Park E. Structural basis of mitochondrial protein import by the TIM23 complex. Nature. PMID 37344598 DOI: 10.1038/s41586-023-06239-6 |
0.322 |
|
| 2023 |
Li Y, Acharya A, Yang L, Liu J, Tajkhorshid E, Zgurskaya HI, Jackson M, Gumbart JC. Insights into substrate transport and water permeation in the mycobacterial transporter MmpL3. Biophysical Journal. PMID 36926696 DOI: 10.1016/j.bpj.2023.03.018 |
0.634 |
|
| 2022 |
Pang YT, Acharya A, Lynch DL, Pavlova A, Gumbart JC. SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact. Communications Biology. 5: 1170. PMID 36329138 DOI: 10.1038/s42003-022-04138-6 |
0.567 |
|
| 2022 |
Allsopp R, Pavlova A, Cline T, Salyapongse AM, Gillilan RE, Di YP, Deslouches B, Klauda JB, Gumbart JC, Tristram-Nagle S. Antimicrobial Peptide Mechanism Studied by Scattering-Guided Molecular Dynamics Simulation. The Journal of Physical Chemistry. B. PMID 36067064 DOI: 10.1021/acs.jpcb.2c03193 |
0.321 |
|
| 2022 |
Hermansen S, Ryoo D, Orwick-Rydmark M, Saragliadis A, Gumbart JC, Linke D. The Role of Extracellular Loops in the Folding of Outer Membrane Protein X (OmpX) of . Frontiers in Molecular Biosciences. 9: 918480. PMID 35911955 DOI: 10.3389/fmolb.2022.918480 |
0.38 |
|
| 2022 |
Stevens CM, Babii SO, Pandya AN, Li W, Li Y, Mehla J, Scott R, Hegde P, Prathipati PK, Acharya A, Liu J, Gumbart JC, North J, Jackson M, Zgurskaya HI. Proton transfer activity of the reconstituted MmpL3 is modulated by substrate mimics and inhibitors. Proceedings of the National Academy of Sciences of the United States of America. 119: e2113963119. PMID 35858440 DOI: 10.1073/pnas.2113963119 |
0.609 |
|
| 2022 |
Yu B, Roy Choudhury M, Yang X, Benoit SL, Womack E, Van Mouwerik Lyles K, Acharya A, Kumar A, Yang C, Pavlova A, Zhu M, Yuan Z, Gumbart JC, Boykin DW, Maier RJ, et al. Restoring and Enhancing the Potency of Existing Antibiotics against Drug-Resistant Gram-Negative Bacteria through the Development of Potent Small-Molecule Adjuvants. Acs Infectious Diseases. PMID 35801980 DOI: 10.1021/acsinfecdis.2c00121 |
0.54 |
|
| 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 |
0.563 |
|
| 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 |
0.502 |
|
| 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 |
0.36 |
|
| 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 |
0.513 |
|
| 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 |
0.568 |
|
| 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 |
0.576 |
|
| 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 |
0.518 |
|
| 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 |
0.53 |
|
| 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 |
0.352 |
|
| 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 |
0.399 |
|
| 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 |
0.624 |
|
| 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 |
0.621 |
|
| 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 |
0.356 |
|
| 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 |
0.356 |
|
| 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 |
0.623 |
|
| 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 |
0.67 |
|
| 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 |
0.399 |
|
| 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 |
0.34 |
|
| 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 |
0.635 |
|
| 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 |
Kuo KM, Lundquist K, Gumbart JC. Interrogating the Hybrid-barrel Model of Bacterial Outer Membrane Protein Biogenesis by the BAM Complex Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.2102 |
0.42 |
|
| 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 |
0.304 |
|
| 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 |
0.591 |
|
| 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 |
0.587 |
|
| 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 |
0.446 |
|
| 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 |
0.345 |
|
| 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 |
0.444 |
|
| 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 |
0.356 |
|
| 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 |
0.388 |
|
| 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 |
0.333 |
|
| 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 |
0.443 |
|
| 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 |
0.361 |
|
| 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 |
0.676 |
|
| 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 |
0.434 |
|
| 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 |
0.381 |
|
| 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 |
0.335 |
|
| 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 |
0.345 |
|
| 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 |
0.624 |
|
| 2017 |
Gumbart JC. Producing membrane proteins one simulation at a time. The Journal of Biological Chemistry. 292: 19546-19547. PMID 29175817 DOI: 10.1074/Jbc.H117.813469 |
0.453 |
|
| 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 |
0.356 |
|
| 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 |
0.425 |
|
| 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 |
0.309 |
|
| 2017 |
Noinaj N, Gumbart JC, Buchanan SK. The β-barrel assembly machinery in motion. Nature Reviews. Microbiology. PMID 28216659 DOI: 10.1107/S0108767317097380 |
0.42 |
|
| 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 |
0.337 |
|
| 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 |
0.47 |
|
| 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 |
0.32 |
|
| 2017 |
Hwang S, Gumbart JC. Engineering the Cell Envelope of Gram-Negative Bacteria Biophysical Journal. 112: 309a. DOI: 10.1016/J.Bpj.2016.11.1675 |
0.433 |
|
| 2017 |
Hazel A, Gumbart JC. Examining the Stability of β-Sheets using the Charmm Drude Polarizable Force Field Biophysical Journal. 112: 197a. DOI: 10.1016/J.Bpj.2016.11.1093 |
0.349 |
|
| 2016 |
Balusek C, Gumbart JC. Role of the Native Outer-Membrane Environment on the Transporter BtuB. Biophysical Journal. 111: 1409-1417. PMID 27705764 DOI: 10.1016/J.Bpj.2016.08.033 |
0.389 |
|
| 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 |
0.521 |
|
| 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 |
0.348 |
|
| 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 |
0.409 |
|
| 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 |
0.584 |
|
| 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 |
0.677 |
|
| 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 |
0.489 |
|
| 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 |
0.485 |
|
| 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 |
0.337 |
|
| 2016 |
Korablyov M, Pavlova A, Gumbart J. Rational Development of a New Type of HBV Capsid Inhibitors by a Combination of Microsecond-Scale Molecular Dynamics and Docking Biophysical Journal. 110: 177a-178a. DOI: 10.1016/J.Bpj.2015.11.991 |
0.337 |
|
| 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 |
0.426 |
|
| 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 |
Hazel A, Gumbart JC. Examining the Vectorial Folding Pathway of the β-Helical Peptide, Pertactin, using Molecular Dynamics Simulations Biophysical Journal. 110: 390a. DOI: 10.1016/J.Bpj.2015.11.2107 |
0.39 |
|
| 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 |
0.424 |
|
| 2016 |
Hwang H, Gumbart JC. In Silico Measurement of the Mechanical Properties of Realistic Bacterial Inner and Outer Membranes Biophysical Journal. 110: 370a. DOI: 10.1016/J.Bpj.2015.11.1995 |
0.425 |
|
| 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 |
0.32 |
|
| 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 |
0.31 |
|
| 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 |
0.432 |
|
| 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 |
0.389 |
|
| 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 |
0.309 |
|
| 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 |
0.388 |
|
| 2015 |
Hazel A, Gumbart JC. Thermodynamics of β-Structures from Molecular Dynamics Simulations Biophysical Journal. 108: 518a. DOI: 10.1016/J.Bpj.2014.11.2841 |
0.387 |
|
| 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 |
0.479 |
|
| 2015 |
Balusek C, Gumbart JC. Unfolding the Luminal Domain of BtuB in a Native Bilayer Biophysical Journal. 108: 202a. DOI: 10.1016/J.Bpj.2014.11.1118 |
0.435 |
|
| 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 |
0.373 |
|
| 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 |
0.461 |
|
| 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 |
0.658 |
|
| 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 |
0.512 |
|
| 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 |
0.36 |
|
| 2014 |
Noinaj N, Kuszak A, Balusek C, Gumbart J, Lukacik P, Chang H, Easley N, Lithgow T, Buchanan S. The role of BamA in the biogenesis of beta-barrel membrane proteins Acta Crystallographica Section a Foundations and Advances. 70: C578-C578. DOI: 10.1107/S2053273314094212 |
0.392 |
|
| 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 |
0.477 |
|
| 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 |
0.326 |
|
| 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 |
0.659 |
|
| 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 |
0.498 |
|
| 2014 |
Hazel A, Gumbart JC. Computational Methods for Measuring the Free Energy of Folding in the Ribosomal Exit Tunnel Biophysical Journal. 106: 257a. DOI: 10.1016/J.Bpj.2013.11.1510 |
0.38 |
|
| 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 |
0.538 |
|
| 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 |
0.791 |
|
| 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 |
0.472 |
|
| 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 |
0.385 |
|
| 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 |
0.364 |
|
| 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 |
0.682 |
|
| 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 |
0.509 |
|
| 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 |
0.327 |
|
| 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: 10.1007/978-1-62703-023-6_19 |
0.402 |
|
| 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 |
0.512 |
|
| 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 |
0.596 |
|
| 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 |
0.328 |
|
| 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 |
0.393 |
|
| 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 |
0.815 |
|
| 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 |
0.782 |
|
| 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 |
0.667 |
|
| 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 |
0.483 |
|
| 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 |
0.573 |
|
| 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 |
0.601 |
|
| 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 |
0.586 |
|
| 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 |
0.796 |
|
| 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 |
0.427 |
|
| 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 |
0.713 |
|
| 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 |
0.577 |
|
| 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 |
0.737 |
|
| 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 |
0.588 |
|
| 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 |
0.73 |
|
| 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 |
0.53 |
|
| 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 |
0.795 |
|
| 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 |
0.354 |
|
| 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 |
0.812 |
|
| 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 |
0.8 |
|
| 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 |
0.325 |
|
| 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 |
0.539 |
|
| 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 |
0.748 |
|
| 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 |
0.572 |
|
| 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 |
0.419 |
|
| 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 |
0.554 |
|
| 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 |
0.741 |
|
| 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 |
0.624 |
|
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