J. Gumbart

发表

Scalable molecular dynamics with NAMD

Laxmikant V. Kalé, Klaus Schulten, Wei Wang, 2005, J. Comput. Chem..

Molecular dynamics simulations of proteins in lipid bilayers.

Klaus Schulten, Yi Wang, James Gumbart, 2005, Current opinion in structural biology.

Cryo–EM structure of the ribosome–SecYE complex in the membrane environment

Klaus Schulten, Marco Gartmann, Thomas Becker, 2011, Nature Structural &Molecular Biology.

Structural insight into the biogenesis of β-barrel membrane proteins

Trevor Lithgow, Nicholas Noinaj, James C. Gumbart, 2013, Nature.

Living on the edge: Simulations of bacterial outer-membrane proteins.

James C Gumbart, Hyea Hwang, Anna Pavlova, 2016, Biochimica et biophysica acta.

Mechanics of force propagation in TonB-dependent outer membrane transport.

James Gumbart, Emad Tajkhorshid, E. Tajkhorshid, 2007, Biophysical journal.

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

J. Gumbart, C. Balusek, 2016, Biophysical journal.

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

John A. Gunnels, Julie C. Mitchell, Matthew B. Baker, 2020, ChemRxiv.

Applications of the molecular dynamics flexible fitting method.

Leonardo G. Trabuco, K. Schulten, E. Villa, 2011, Journal of structural biology.

Constant electric field simulations of the membrane potential illustrated with simple systems.

B. Roux, M. Sotomayor, J. Gumbart, 2012, Biochimica et biophysica acta.

Inhibitor Binding Influences the Protonation State of Histidines in SARS-CoV-2 Main Protease

Jerry M. Parks, Jeremy C. Smith, Callum J. Dickson, 2020, bioRxiv.

Molecular dynamics simulations of membrane channels and transporters.

K. Schulten, E. Tajkhorshid, M. Sotomayor, 2009, Current opinion in structural biology.

Thermodynamics of Deca-alanine Folding in Water

Christophe Chipot, James C. Gumbart, Anthony Hazel, 2014, Journal of chemical theory and computation.

Case Study : Light Harvesting Complex II

Danielle E. Chandler, J. Gumbart, J. Hsin, 2008 .

Long time and large size molecular dynamics simulations made feasible through new TeraGrid hardware and software

James C. Phillips, Peter L. Freddolino, Kirby L. Vandivort, 2008 .

Reconciling the Roles of Kinetic and Thermodynamic Factors in Membrane–Protein Insertion

K. Schulten, B. Roux, J. Gumbart, 2013, Journal of the American Chemical Society.

Free energy of nascent-chain folding in the translocon.

K. Schulten, C. Chipot, J. Gumbart, 2011, Journal of the American Chemical Society.

Toward the rational design of macrolide antibiotics to combat resistance

Jerry M. Parks, J. Gumbart, J. Parks, 2017, Chemical biology & drug design.

Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds

Yi Wang, Robert V. Swift, Rommie E. Amaro, 2016, J. Chem. Inf. Model..

Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2

Jerry M. Parks, C. Chipot, J. Gumbart, 2021, Biophysical Journal.

Dynamic Behavior of Trigger Factor on the Ribosome.

K. Schulten, J. Gumbart, W. Han, 2016, Journal of Molecular Biology.

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

C. Chipot, J. Gumbart, 2016, Biochimica et biophysica acta.

Mechanisms of SecM-mediated stalling in the ribosome.

Daniel N. Wilson, K. Schulten, J. Gumbart, 2012, Biophysical journal.

Distribution of mechanical stress in the Escherichia coli cell envelope.

Jerry M. Parks, J. Gumbart, J. Lakey, 2018, Biochimica et biophysica acta. Biomembranes.

Parameterization of a drug molecule with a halogen σ-hole particle using ffTK: Implementation, testing, and comparison.

E. Tajkhorshid, J. Gumbart, A. Pavlova, 2020, The Journal of chemical physics.

Structure and misfolding of the flexible tripartite coiled coil domain of glaucoma-associated myocilin

R. L. Lieberman, J. Gumbart, S. Hill, 2017, bioRxiv.

Structure and misfolding of the flexible tripartite coiled coil domain of glaucoma-associated myocilin

R. L. Lieberman, J. Gumbart, S. Hill, 2017, bioRxiv.

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

John A. Gunnels, Julie C. Mitchell, Matthew B. Baker, 2020, Journal of chemical information and modeling.

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

S. Harvey, T. Cheatham, Xiang-Jun Lu, 2016, The journal of physical chemistry. B.

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

Jerry M. Parks, J. Gumbart, J. Parks, 2018, Journal of chemical theory and computation.

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

Duncan Poole, John A. Gunnels, Arvind Ramanathan, 2020, J. Chem. Inf. Model..

Identification of Binding Sites for Efflux Pump Inhibitors of the AcrAB-TolC Component AcrA.

Jerry M. Parks, A. T. Green, Jeremy C. Smith, 2019, Biophysical journal.

Stepwise gating of the Sec61 protein-conducting channel by Sec63 and Sec62

J. Gumbart, E. Park, S. Itskanov, 2020, bioRxiv.

Conformational Changes of the Clamp of the Protein Translocation ATPase SecA.

T. Rapoport, J. Gumbart, Yu Chen, 2015, Journal of molecular biology.

Accelerating Membrane Simulations with Hydrogen Mass Repartitioning Hydrogen

J. Gumbart, Hyea Hwang, K. Lundquist, 2020 .

When the Dust Has Settled: Calculation of Binding Affinities from First Principles for SARS-CoV-2 Variants with Quantitative Accuracy

C. Chipot, J. Gumbart, Haochuan Chen, 2022, Journal of chemical theory and computation.

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

J. Gumbart, N. Noinaj, K. Lundquist, 2018, Proceedings of the National Academy of Sciences.

Synergistic Biophysical Techniques Reveal Structural Mechanisms of Engineered Cationic Antimicrobial Peptides in Lipid Model Membranes.

A. Salyapongse, J. Gumbart, D. Huster, 2020, Chemistry.

IcmQ in the Type 4b secretion system contains a novel NAD + binding domain

C. Akey, J. Gumbart, I. V. Akey, 2013 .

Restoring and Enhancing the Potency of Existing Antibiotics against Drug-Resistant Gram-Negative Bacteria through the Development of Potent Small-Molecule Adjuvants.

J. Gumbart, Arvind Kumar, D. Boykin, 2022, ACS infectious diseases.

Point Mutations in TbpA Abrogate Human Transferrin Binding in Neisseria gonorrhoeae

J. Gumbart, N. Noinaj, K. Lundquist, 2022, Infection and immunity.

A new crystal form of MshB from Mycobacterium tuberculosis with glycerol and acetate in the active site suggests the catalytic mechanism.

D. J. Steenkamp, B. Sewell, J. Gumbart, 2012, Acta crystallographica. Section D, Biological crystallography.

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

Robert J A Goode, T. Lithgow, J. Gumbart, 2017, Molecular microbiology.

Antimicrobial Peptide Mechanism Studied by Scattering-Guided Molecular Dynamics Simulation.

Jeffery B. Klauda, A. Salyapongse, R. Gillilan, 2022, The journal of physical chemistry. B.

Bifunctional Janus Particles as Multivalent Synthetic Nanoparticle Antibodies (SNAbs) for Selective Depletion of Target Cells.

Kelsey P. Kubelick, S. Emelianov, Younan Xia, 2021, Nano letters.

Point Mutations in TbpA Abrogate Human Transferrin Binding in Neisseria gonorrhoeae

J. Gumbart, N. Noinaj, K. Lundquist, 2022, Infection and immunity.

β-Barrel Proteins Tether the Outer Membrane in Many Gram-Negative Bacteria

Jerry M. Parks, Ankur V Patel, R. Heinzen, 2020, Nature microbiology.

Molecular basis for the activation of a catalytic asparagine residue in a self-cleaving bacterial autotransporter.

E. Tajkhorshid, S. Buchanan, J. Gumbart, 2012, Journal of molecular biology.

The β-barrel assembly machinery in motion

S. Buchanan, J. Gumbart, N. Noinaj, 2017, Nature Reviews Microbiology.

Outer membrane protein size and LPS O-antigen define protective antibody targeting to the Salmonella surface

I. Henderson, A. Cunningham, J. Gumbart, 2020, Nature Communications.

Resolving the Hydride Transfer Pathway in Oxidative Conversion of Proline to Pyrrole.

J. Gumbart, A. Pavlova, Dongqi Yi, 2021, Biochemistry.

Rapid parameterization of small molecules using the force field toolkit

Klaus Schulten, Jan Saam, Emad Tajkhorshid, 2013, J. Comput. Chem..

Structure and Function of Tryptophan–Tyrosine Dyads in Biomimetic β Hairpins

J. Perry, C. Pagba, J. Gumbart, 2019, The journal of physical chemistry. B.

Redox-Driven Conformational Dynamics in a Photosystem-II-Inspired β-Hairpin Maquette Determined through Spectroscopy and Simulation.

C. Pagba, J. Gumbart, A. Pavlova, 2017, The journal of physical chemistry. B.

Structure of the SecY channel during initiation of protein translocation

T. Rapoport, S. Ludtke, C. Akey, 2013, Nature.

Quantifying arrhythmic long QT effects of hydroxychloroquine and azithromycin with whole-heart optical mapping and simulations

F. Fenton, E. Cherry, H. Ashikaga, 2021, Heart rhythm O2.

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

N. Majdalani, S. Buchanan, J. Gumbart, 2016, Structure.

Adaptation of the periplasm to maintain spatial constraints essential for cell envelope processes and cell viability

T. Lithgow, M. Beeby, J. Gumbart, 2022, eLife.

Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein

A. J. Higgins, M. Moniruzzaman, J. Gumbart, 2022, bioRxiv.

Non-detergent isolation of a cyanobacterial photosystem I using styrene maleic acid alternating copolymers

J. Gumbart, M. Li, B. Bruce, 2019, RSC advances.

The Mechanism of Action of Hepatitis B Virus Capsid Assembly Modulators Can Be Predicted from Binding to Early Assembly Intermediates.

C. Chipot, R. Schinazi, J. Gumbart, 2022, Journal of medicinal chemistry.

Critical interactions for SARS-CoV-2 spike protein binding to ACE2 identified by machine learning

Jerry M. Parks, C. Chipot, J. Gumbart, 2021, bioRxiv.

A novel human IL2RB mutation results in T and NK cell–driven immune dysregulation

Ryan M. Baxter, Noor B. Dawany, J. Kelsen, 2019, The Journal of experimental medicine.

Comprehensive structure and functional adaptations of the yeast nuclear pore complex

B. Chait, A. Sali, S. Jaspersen, 2021, Cell.

Preparing Membrane Proteins for Simulation Using CHARMM-GUI.

J. Gumbart, Yupeng Li, Jinchan Liu, 2021, Methods in molecular biology.

Structural basis for iron piracy by pathogenic Neisseria

E. Tajkhorshid, A. Steven, A. Mason, 2012, Nature.

DNA Scrunching in the Packaging of Viral Genomes.

S. Harvey, Xiang-Jun Lu, Harold D. Kim, 2016, The journal of physical chemistry. B.

Architecture and assembly of the Gram‐positive cell wall

Benoît Roux, Grant J Jensen, Morgan Beeby, 2013, Molecular microbiology.

The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask

Christophe Chipot, Jeffrey Comer, Andrew Pohorille, 2014, The journal of physical chemistry. B.

Structure of Monomeric Yeast and Mammalian Sec61 Complexes Interacting with the Translating Ribosome

Klaus Schulten, Eric Westhof, Shashi Bhushan, 2009, Science.

BamA is required for autotransporter secretion.

D. Linke, J. Gumbart, K. Lundquist, 2020, Biochimica et biophysica acta. General subjects.

Lateral opening and exit pore formation are required for BamA function.

S. Buchanan, J. Gumbart, N. Noinaj, 2014, Structure.

The Mechanism of the Amidases

B. Sewell, J. Gumbart, D. Cowan, 2013, The Journal of Biological Chemistry.

Plasticity within the barrel domain of BamA mediates a hybrid-barrel mechanism by BAM

T. Klose, J. Gumbart, T. White, 2021, Nature Communications.

Parametrization of macrolide antibiotics using the force field toolkit

Anna Pavlova, James C Gumbart, J. Gumbart, 2015, J. Comput. Chem..

Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease

Callum J. Dickson, C. Chipot, J. Gumbart, 2020, Chemical science.

Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations

Grant J. Jensen, Benoît Roux, James C. Gumbart, 2014, PLoS Comput. Biol..

Combinatorial phosphorylation modulates the structure and function of the G protein γ subunit in yeast

J. Gumbart, Yui Tik Pang, Wei Li, 2021, Science Signaling.

Combinatorial phosphorylation modulates the structure and function of the G protein gamma subunit in yeast

J. Gumbart, Yui Tik Pang, Wei Li, 2020, bioRxiv.

Structural and biophysical characterization of an epitope-specific engineered Fab fragment and complexation with membrane proteins: implications for co-crystallization.

J. Gumbart, Sibel Kalyoncu, J. Maynard, 2015, Acta crystallographica. Section D, Biological crystallography.

Weak tension accelerates hybridization and dehybridization of short oligonucleotides

Harold D. Kim, J. Gumbart, D. J. Hart, 2022, bioRxiv.

Presence of substrate aids lateral gate separation in LptD.

J. Gumbart, K. Lundquist, 2020, Biochimica et biophysica acta. Biomembranes.

Folding and Insertion of Transmembrane Helices at the ER

J. Gumbart, P. Whitley, I. Mingarro, 2021, International journal of molecular sciences.

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

S. White, J. Gumbart, M. Ulmschneider, 2018, The Journal of Membrane Biology.

Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations

B. Roux, J. Gumbart, Fatemeh Khalili-Araghi, 2013, The Journal of general physiology.

SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact

J. Gumbart, A. Pavlova, D. Lynch, 2021, bioRxiv.

Stable calcium-free myocilin olfactomedin domain variants reveal challenges in differentiating between benign and glaucoma-causing mutations

J. Gumbart, C. Dickey, S. Hill, 2019, The Journal of Biological Chemistry.

Structural insight into toxin secretion by contact-dependent growth inhibition transporters

S. Buchanan, J. Gumbart, K. Lundquist, 2020, eLife.

Membrane thinning and lateral gating are consistent features of BamA across multiple species

J. Gumbart, Jinchan Liu, 2020, PLoS Comput. Biol..

Diverse Protein-Folding Pathways and Functions of β-Hairpins and β-Sheets

J. Gumbart, A. Pavlova, Hyea Hwang, 2018 .

Coupling of calcium and substrate binding through loop alignment in the outer-membrane transporter BtuB.

E. Tajkhorshid, J. Gumbart, M. Wiener, 2009, Journal of molecular biology.

Joint neutron/molecular dynamics vibrational spectroscopy reveals softening of HIV-1 protease upon binding of a tight inhibitor.

L. Daemen, J. Gumbart, A. Kovalevsky, 2022, Physical Chemistry, Chemical Physics - PCCP.

Symmetry-restrained flexible fitting for symmetric EM maps.

Klaus Schulten, Kwok-Yan Chan, James Gumbart, 2011, Structure.

Molecular dynamics studies of the archaeal translocon.

Klaus Schulten, James Gumbart, K. Schulten, 2006, Biophysical journal.

Gatekeeping Ketosynthases Dictate Initiation of Assembly Line Biosynthesis of Pyrrolic Polyketides.

Will R. Gutekunst, J. Gumbart, Dongqi Yi, 2021, Journal of the American Chemical Society.

Standard binding free energies from computer simulations: What is the best strategy?

Christophe Chipot, Benoît Roux, James C Gumbart, 2013, Journal of chemical theory and computation.

Self-assembly of photosynthetic membranes.

Klaus Schulten, Melih Sener, Christopher B Harrison, 2010, Chemphyschem : a European journal of chemical physics and physical chemistry.

A Novel Approach to Simulating the Gating Transitions of Mechanosensitive Channels.

J. Gumbart, 2020, Biophysical journal.

Membrane curvature induced by aggregates of LH2s and monomeric LH1s.

Danielle E. Chandler, K. Schulten, C. Chipot, 2009, Biophysical journal.

Protein-induced membrane curvature investigated through molecular dynamics flexible fitting.

Klaus Schulten, Pu Qian, James Gumbart, 2009, Biophysical journal.

Tuning Proton Transfer Thermodynamics in SARS-CoV-2 Main Protease: Implications for Catalysis and Inhibitor Design

Jeremy C. Smith, C. Chipot, J. Gumbart, 2021, The journal of physical chemistry letters.

Accelerating Membrane Simulations with Hydrogen Mass Repartitioning.

J. Gumbart, A. Pavlova, Hyea Hwang, 2019, Journal of chemical theory and computation.

β-Barrel proteins tether the outer membrane in many Gram-negative bacteria

Jerry M. Parks, R. Heinzen, J. Gumbart, 2020, Nature Microbiology.

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

G. Jensen, J. Gumbart, L. Nguyen, 2016, Methods in molecular biology.

Coarse-grained simulations of bacterial cell wall growth reveal that local coordination alone can be sufficient to maintain rod shape

G. Jensen, M. Beeby, J. Gumbart, 2015, Proceedings of the National Academy of Sciences.

Efficient determination of protein-protein standard binding free energies from first principles.

Christophe Chipot, Benoît Roux, James C Gumbart, 2013, Journal of chemical theory and computation.

Resolving large conformational change pathways through machine learning and enhanced sampling simulations

J. Gumbart, Yui Tik Pang, 2022, Biophysical Journal.

Conformational dynamics of AcrA govern multidrug efflux pump assembly.

Jerry M. Parks, Jeremy C. Smith, J. Gumbart, 2019, ACS infectious diseases.

Lpp positions peptidoglycan at the AcrA-TolC interface in the AcrAB-TolC multidrug efflux pump.

Jerry M. Parks, Jeremy C. Smith, M. Beeby, 2021, Biophysical journal.

ACE2 glycans preferentially interact with SARS-CoV-2 over SARS-CoV.

J. Gumbart, A. Pavlova, D. Lynch, 2021, Chemical communications.

Species-agnostic polymeric formulations for inhalable messenger RNA delivery to the lung

C. Zurla, J. Gumbart, R. Guerrero-Ferreira, 2022, Nature Materials.

Fatal arrhythmias: Another reason why doctors remain cautious about chloroquine/hydroxychloroquine for treating COVID-19

F. Fenton, E. Cherry, H. Ashikaga, 2020, Heart Rhythm.

Proton transfer activity of the reconstituted Mycobacterium tuberculosis MmpL3 is modulated by substrate mimics and inhibitors

P. Prathipati, J. Gumbart, H. Zgurskaya, 2022, Proceedings of the National Academy of Sciences of the United States of America.

Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations

C. Chipot, W. Cai, J. Gumbart, 2022, Nature Protocols.

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

Haohao Fu, Christophe Chipot, Xueguang Shao, 2018, J. Chem. Inf. Model..

Tuning proton transfer thermodynamics in SARS-Cov-2 main protease: implications for catalysis and inhibitor design

Jeremy C. Smith, C. Chipot, J. Gumbart, 2020, ChemRxiv : the preprint server for chemistry.

Structural determinants of lateral gate opening in the protein translocon.

K. Schulten, J. Gumbart, 2007, Biochemistry.

Understanding Virus Structure and Dynamics through Molecular Simulations

J. Gumbart, D. Lynch, A. Pavlova, 2023, Journal of chemical theory and computation.

Stepwise gating of the Sec61 protein-conducting channel by Sec63 and Sec62

J. Gumbart, E. Park, S. Itskanov, 2021, Nature Structural & Molecular Biology.

ATP-Dependent Signaling in Simulations of a Revised Model of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR).

J. Gumbart, N. McCarty, I. Schmidt-Krey, 2019, The journal of physical chemistry. B.

The mobility of two kinase domains in the Escherichia coli chemoreceptor array varies with signalling state

Ariane Briegel, J. S. Parkinson, Catherine M. Oikonomou, 2013, Molecular microbiology.

Regulation of the protein-conducting channel by a bound ribosome.

Klaus Schulten, James Gumbart, Elizabeth Villa, 2009, Structure.

The Role of Extracellular Loops in the Folding of Outer Membrane Protein X (OmpX) of Escherichia coli

D. Linke, J. Gumbart, D. Ryoo, 2022, Frontiers in Molecular Biosciences.

Transmembrane but not soluble helices fold inside the ribosome tunnel

G. von Heijne, I. Nilsson, J. Gumbart, 2018, Nature Communications.

The Roles of Pore Ring and Plug in the SecY Protein-conducting Channel

K. Schulten, J. Gumbart, 2008, The Journal of general physiology.

A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins

Peng Lian, Jeremy C. Smith, Jeremy C Smith, 2019, J. Comput. Chem..

Intrinsic curvature properties of photosynthetic proteins in chromatophores.

Klaus Schulten, Christopher B Harrison, James Gumbart, 2008, Biophysical journal.

IcmQ in the Type 4b secretion system contains an NAD+ binding domain.

C. Akey, J. Gumbart, I. V. Akey, 2013, Structure.

Extraction of Dielectric Permittivity from Atomistic Molecular Dynamics Simulations and Microwave Measurements.

J. Gumbart, D. Ryoo, Zijian Zhang, 2022, The journal of physical chemistry. B.

Producing membrane proteins one simulation at a time

J. Gumbart, 2017, The Journal of Biological Chemistry.

The Effect of (-)-Epigallocatechin-3-Gallate on the Amyloid-β Secondary Structure.

K. Gerwert, J. Gumbart, V. Batista, 2020, Biophysical journal.

Tyrosine, cysteine, and proton coupled electron transfer in a ribonucleotide reductase-inspired beta hairpin maquette.

J. Perry, C. Pagba, J. Gumbart, 2019, Chemical communications.

Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD

Lei Huang, Klaus Schulten, Wei Jiang, 2014, Comput. Phys. Commun..

Determination of membrane-insertion free energies by molecular dynamics simulations.

B. Roux, J. Gumbart, 2012, Biophysical journal.

N-terminal intrinsic disorder is an ancestral feature of Gγ subunits that influences the balance between different Gβγ signaling axes in yeast

J. Gumbart, Yui Tik Pang, Wei Li, 2023, The Journal of biological chemistry.

Mechanism of action of HBV capsid assembly modulators predicted from binding to early assembly intermediates

C. Chipot, R. Schinazi, J. Gumbart, 2020, bioRxiv.

Drug Binding to BamA Targets Its Lateral Gate

J. Gumbart, Katie M. Kuo, Jinchan Liu, 2023, The journal of physical chemistry. B.

Free-energy cost for translocon-assisted insertion of membrane proteins

Klaus Schulten, Christophe Chipot, James Gumbart, 2011, Proceedings of the National Academy of Sciences.

ACE2 glycans preferentially interact with the RBD of SARS-CoV-2 over SARS-CoV

J. Gumbart, A. Pavlova, D. Lynch, 2021, bioRxiv.

Exploring adsorption of neutral aromatic pollutants onto graphene nanomaterials via molecular dynamics simulations and theoretical linear solvation energy relationships

J. Gumbart, Zhongfang Chen, Jingwen Chen, 2018 .

Molecular basis for inhibition of methane clathrate growth by a deep subsurface bacterial protein

J. Gumbart, J. Glass, R. Drori, 2023, PNAS nexus.

Molecular Machines in Biology: Viewing the Mechanisms of Translation through the Computational Microscope

Klaus Schulten, James C. Gumbart, Eduard Schreiner, 2011 .

Constant electric field simulations of the membrane potential illustrated with simple systems.

B. Roux, M. Sotomayor, J. Gumbart, 2012, Biochimica et biophysica acta.

Molecular dynamics simulations of proteins in lipid bilayers.

K. Schulten, E. Tajkhorshid, J. Gumbart, 2005, Current opinion in structural biology.

A partial human LCK defect causes a T cell immunodeficiency with intestinal inflammation

Ryan M. Baxter, U. Pannicke, A. Schulz, 2023, The Journal of experimental medicine.

Enhanced surface accessibility of SARS-CoV-2 Omicron spike protein due to an altered glycosylation profile

J. Gumbart, Jakub Baudys, Zijian Zhang, 2023, bioRxiv.

Transmembrane but not soluble helices fold inside the ribosome tunnel

G. von Heijne, I. Nilsson, J. Gumbart, 2018, Nature Communications.

A Rigorous Framework for Calculating Protein-Protein Binding Affinities in Membranes.

J. Gumbart, Haochuan Chen, Marharyta Blazhynska, 2023, Journal of chemical theory and computation.

The Mechanism of the Amidases

B. Sewell, J. Gumbart, A. Varsani, 2013, The Journal of Biological Chemistry.

Structural basis of mitochondrial protein import by the TIM23 complex

J. Gumbart, Yuanyuan Chen, E. Park, 2023, Nature.

Enhanced Surface Accessibility of SARS-CoV-2 Omicron Spike Protein Due to an Altered Glycosylation Profile

J. Gumbart, Jakub Baudys, Zijian Zhang, 2024, ACS infectious diseases.