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Author Details

James C Gumbart
Georgia Institute of Technology
2005
139
39
Andrej Sali (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37962568A partial human LCK defect causes a T cell immunodeficiency with intestinal inflammation.J Exp Med2024
36563291Structural Determinants of Indole-2-carboxamides: Identification of Lead Acetamides with Pan Antimycobacterial Activity.J Med Chem2023
37587651Drug Binding to BamA Targets Its Lateral Gate.J Phys Chem B2023
37644917Molecular basis for inhibition of methane clathrate growth by a deep subsurface bacterial protein.PNAS Nexus2023
37538992Toward a 3D physical model of diffusive polymer chains.Front Phys2023
38091976A Rigorous Framework for Calculating Protein-Protein Binding Affinities in Membranes.J Chem Theory Comput2023
37354971N-terminal intrinsic disorder is an ancestral feature of Gγ subunits that influences the balance between different Gβγ signaling axes in yeast.J Biol Chem2023
37192279Understanding Virus Structure and Dynamics through Molecular Simulations.J Chem Theory Comput2023
37344598Structural basis of mitochondrial protein import by the TIM23 complex.Nature2023
37463890Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein.Nat Commun2023
36960532Uncovering the folding mechanism of pertactin: A comparative study of isolated and vectorial folding.Biophys J2023
36926696Insights into substrate transport and water permeation in the mycobacterial transporter MmpL3.Biophys J2023
36443576Species-agnostic polymeric formulations for inhalable messenger RNA delivery to the lung.Nat Mater2023
36869666Weak tension accelerates hybridization and dehybridization of short oligonucleotides.Nucleic Acids Res2023
35084330Adaptation of the periplasm to maintain spatial constraints essential for cell envelope processes and cell viability.Elife2022
35801980Restoring and Enhancing the Potency of Existing Antibiotics against Drug-Resistant Gram-Negative Bacteria through the Development of Potent Small-Molecule Adjuvants.ACS Infect Dis2022
35858440Proton transfer activity of the reconstituted <i>Mycobacterium tuberculosis</i> MmpL3 is modulated by substrate mimics and inhibitors.Proc Natl Acad Sci U S A2022
35911955The Role of Extracellular Loops in the Folding of Outer Membrane Protein X (OmpX) of <i>Escherichia coli</i>.Front Mol Biosci2022
36108303When the Dust Has Settled: Calculation of Binding Affinities from First Principles for SARS-CoV-2 Variants with Quantitative Accuracy.J Chem Theory Comput2022
36067064Antimicrobial Peptide Mechanism Studied by Scattering-Guided Molecular Dynamics Simulation.J Phys Chem B2022
36171073Extraction of Dielectric Permittivity from Atomistic Molecular Dynamics Simulations and Microwave Measurements.J Phys Chem B2022
35927955Modeling intermediates of BamA folding an outer membrane protein.Biophys J2022
36321833Point Mutations in TbpA Abrogate Human Transferrin Binding in Neisseria gonorrhoeae.Infect Immun2022
35290049The Mechanism of Action of Hepatitis B Virus Capsid Assembly Modulators Can Be Predicted from Binding to Early Assembly Intermediates.J Med Chem2022
34982960Comprehensive structure and functional adaptations of the yeast nuclear pore complex.Cell2022
35072459Resolving the Hydride Transfer Pathway in Oxidative Conversion of Proline to Pyrrole.Biochemistry2022
35277695Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations.Nat Protoc2022
35089990Joint neutron/molecular dynamics vibrational spectroscopy reveals softening of HIV-1 protease upon binding of a tight inhibitor.Phys Chem Chem Phys2022
33382974A Novel Approach to Simulating the Gating Transitions of Mechanosensitive Channels.Biophys J2021
33877631Preparing Membrane Proteins for Simulation Using CHARMM-GUI.Methods Mol Biol2021
33900080Tuning Proton Transfer Thermodynamics in SARS-CoV-2 Main Protease: Implications for Catalysis and Inhibitor Design.J Phys Chem Lett2021
33870695Coarse-Grained Simulations of DNA Reveal Angular Dependence of Sticky-End Binding.J Phys Chem B2021
34884581Folding and Insertion of Transmembrane Helices at the ER.Int J Mol Sci2021
34880256Plasticity within the barrel domain of BamA mediates a hybrid-barrel mechanism by BAM.Nat Commun2021
34411576Lpp positions peptidoglycan at the AcrA-TolC interface in the AcrAB-TolC multidrug efflux pump.Biophys J2021
34430945Quantifying arrhythmic long QT effects of hydroxychloroquine and azithromycin with whole-heart optical mapping and simulations.Heart Rhythm O22021
34019602ACE2 glycans preferentially interact with SARS-CoV-2 over SARS-CoV.Chem Commun (Camb)2021
34158397Combinatorial phosphorylation modulates the structure and function of the G protein γ subunit in yeast.Sci Signal2021
33989500Gatekeeping Ketosynthases Dictate Initiation of Assembly Line Biosynthesis of Pyrrolic Polyketides.J Am Chem Soc2021
34097860Inward-facing glycine residues create sharp turns in β-barrel membrane proteins.Biochim Biophys Acta Biomembr2021
34086459Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2.J Phys Chem Lett2021
33139883β-Barrel proteins tether the outer membrane in many Gram-negative bacteria.Nat Microbiol2021
33398175Stepwise gating of the Sec61 protein-conducting channel by Sec63 and Sec62.Nat Struct Mol Biol2021
33395313Bifunctional Janus Particles as Multivalent Synthetic Nanoparticle Antibodies (SNAbs) for Selective Depletion of Target Cells.Nano Lett2021
31351059Presence of substrate aids lateral gate separation in LptD.Biochim Biophys Acta Biomembr2020
35356437Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease.Chem Sci2020
32051408Outer membrane protein size and LPS O-antigen define protective antibody targeting to the Salmonella surface.Nat Commun2020
31721253A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins.J Comput Chem2020
33200117Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19.ChemRxiv2020
33200115Tuning Proton Transfer Thermodynamics in SARS-Cov-2 Main Protease: Implications for Catalysis and Inhibitor Design.ChemRxiv2020
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Collaborators

Emad Tajkhorshid
University of Illinois at Urbana-Champaign
Co-authored papers 11
Grant J Jensen
California Institute of Technology, Brigham Young University
Co-authored papers 5
Elizabeth Villa
University of California San Diego, USA Howard Hughes Medical Institute
Co-authored papers 5
Roland Beckmann
University of Munich
Co-authored papers 4
Christopher W Akey
Boston University, Chobanian and Avedisian School of Medicine
Co-authored papers 3
Michael C Wiener
University of Virginia
Co-authored papers 2
Ross M Kedl
Co-authored papers 2
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University of Pennsylvania
Co-authored papers 2
Stephen H White
Co-authored papers 2
Steven J Ludtke
Baylor College of Medicine
Co-authored papers 2
Tom T Nguyen
Co-authored papers 2
Kangkang Song
University of Massachusetts Chan Medical School
Co-authored papers 1
Robert V Swift
University of California San Diego
Co-authored papers 1
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University of Pittsburgh
Co-authored papers 1
Junjie Wang
The Rockefeller University
Co-authored papers 1
Ignacia Echeverria
University of California san francisco
Co-authored papers 1
Chen Xu
University of Massachusetts Chan Medical School
Co-authored papers 1
Julie C Mitchell
Co-authored papers 1
Shinjae Yoo
Brookhaven National Laboratory
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Alasdair C Steven
National Institutes of Health
Co-authored papers 1
Rommie E Amaro
University of California
Co-authored papers 1
Brian T Chait
The Rockefeller University
Co-authored papers 1
Francois Villinger
Co-authored papers 1
Digvijay Singh
University of California San Diego
Co-authored papers 1
Daniel Salzberg
University of California san francisco
Co-authored papers 1
Joseph M Varberg
Stowers Institute for Medical Research
Co-authored papers 1
Jean-Paul Armache
Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park
Co-authored papers 1
Jay R Unruh
Stowers Institute for Medical Research
Co-authored papers 1
Nael A McCarty
Emory University
Co-authored papers 1
Zulin Yu
Stowers Institute for Medical Research
Co-authored papers 1
Release 1.2