James C. Gumbart

Biochemistry, Genetics and Molecular BiologyComputer ScienceMedicineEnvironmental ScienceMaterials Science

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 70 papers. Top paper: “Comprehensive structure and functional adaptations of the yeast nuclear pore complex”.

Comprehensive structure and functional adaptations of the yeast nuclear pore complex

Cell(2022)10.1016/j.cell.2021.12.015

N/A

4.2DataRank · unranked

191 citations

Digvijay Singh, Christna Ouch, Ignacia Echeverria, Ilona Nudelman, Joseph M. Varberg +18 more

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

Nature Microbiology(2020)10.1038/s41564-020-00798-4

N/A

2.3DataRank · unranked

75 citations

Roger A. Moore, Paul A. Beare, Ankur Patel, Robert E. Smith, Marshall Bern +8 more

Scalable molecular dynamics with NAMD

Journal of Computational Chemistry(2005)10.1002/jcc.20289

N/A

1.5DataRank · unranked

17273 citations

Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa +8 more

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

Nature Communications(2020)10.1038/s41467-020-14655-9

N/A

0.692DataRank · unranked

100 citations

Marisol Pérez-Toledo, Anna E. Schager, Jennifer L. Marshall, Charlotte N. Cook, Saeeda Bobat +19 more

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

Heart Rhythm(2020)10.1016/j.hrthm.2020.05.030

N/A

0.500DataRank · unranked

27 citations

Shahriar Iravanian, Hiroshi Ashikaga, Neal K. Bhatia, Conner Herndon, Abouzar Kaboudian +4 more

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(2022)10.1021/acsinfecdis.2c00121

N/A

0.477DataRank · unranked

23 citations

Manjusha Roy Choudhury, Xiaoxiao Yang, Stéphane L. Benoit, Edroyal Womack, Kristin V. Lyles +12 more

Substrate recognition mechanism of the endoplasmic reticulum-associated ubiquitin ligase Doa10

Nature Communications(2024)10.1038/s41467-024-46409-2

N/A

0.457DataRank · unranked

20 citations

Samuel Itskanov, Diane L. Lynch, Yuanyuan Chen, Aasha Turner, James C. Gumbart +2 more

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

Chemistry - A European Journal(2020)10.1002/chem.202000212

N/A

0.449DataRank · unranked

19 citations

Aria Salyapongse, Akari Kumagai, Fernando G. Dupuy, Karpur Shukla, Anja Penk +8 more

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

The Journal of Experimental Medicine(2023)10.1084/jem.20230927

N/A

0.442DataRank · unranked

18 citations

Manfred Hoenig, Berenice Cabrera-Martinez, Ryan M. Baxter, Josselyn E. Garcia‐Perez, Olivia Bailey +21 more

Comprehensive Structure and Functional Adaptations of the Yeast Nuclear Pore Complex

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.29.466335

N/A

0.406DataRank · unranked

14 citations

Digvijay Singh, Christna Ouch, Ignacia Echeverria, Ilona Nudelman, Joseph M. Varberg +18 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.09.143123

N/A

0.104DataRank · unranked

1 citations

Xinya Su, Shilpa Choudhury, Wei Li, Yui Tik Pang, James C. Gumbart +2 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.09.07.286344

N/A

0.104DataRank · unranked

1 citations

Diane L. Lynch, Isabella Daidone, Laura Zanetti-Polzi, Micholas Dean Smith, Chris Chipot +14 more

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

Biophysical Journal(2021)10.1016/j.bpj.2021.08.016

N/A

0DataRank · unranked

26 citations

Josie L. Ferreira, Hyea Hwang, Anthony Hazel, Connor J. Cooper, Jerry M. Parks +4 more

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

Heart Rhythm O2(2021)10.1016/j.hroo.2021.06.008

N/A

0DataRank · unranked

24 citations

Abouzar Kaboudian, Shahriar Iravanian, Jimena Siles, James C. Gumbart, Hiroshi Ashikaga +5 more

Folding and Insertion of Transmembrane Helices at the ER

International Journal of Molecular Sciences(2021)10.3390/ijms222312778

N/A

0DataRank · unranked

23 citations

Brayan Grau, James C. Gumbart, Luis Martínez‐Gil, Ismael Mingarro, Paul Whitley

Inward-facing glycine residues create sharp turns in β-barrel membrane proteins

Biochimica et Biophysica Acta (BBA) - Biomembranes(2021)10.1016/j.bbamem.2021.183662

N/A

0DataRank · unranked

10 citations

David Ryoo, Curtis Balusek, Atanu Acharya, Marcella Orwick Rydmark, Dirk Linke +2 more

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

Science Signaling(2021)10.1126/scisignal.abd2464

N/A

0DataRank · unranked

7 citations

Xinya Su, Ruth Austin, Shilpa Choudhury, Wei Li, Yui Tik Pang +3 more

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

ChemRxiv(2021)10.26434/chemrxiv.13200227.v2

N/A

0DataRank · unranked

1 citations

Micholas Dean Smith, Chris Chipot, James C. Gumbart, Diane L. Lynch, Anna Pavlova +3 more

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

Nature Protocols(2022)10.1038/s41596-021-00676-1

N/A

0DataRank · unranked

176 citations

Haochuan Chen, Marharyta Blazhynska, Emma Goulard Coderc de Lacam, Florence Szczepaniak, Ànna Pavlova +7 more

Antimicrobial Peptide Mechanism Studied by Scattering-Guided Molecular Dynamics Simulation

The Journal of Physical Chemistry B(2022)10.1021/acs.jpcb.2c03193

N/A

0DataRank · unranked

32 citations

Ànna Pavlova, Tyler Cline, Aria Salyapongse, Richard E. Gillilan, Y. Peter Di +5 more

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

eLife(2022)10.7554/elife.73516

N/A

0DataRank · unranked

30 citations

Christopher J. Stubenrauch, David Ryoo, Hyea Hwang, Eli J Cohen, Von Vergel L Torres +9 more

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

Proceedings of the National Academy of Sciences(2022)10.1073/pnas.2113963119

N/A

0DataRank · unranked

25 citations

Svitlana Babii, Amitkumar N. Pandya, Wei Li, Yupeng Li, Jitender Mehla +10 more

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

Frontiers in Molecular Biosciences(2022)10.3389/fmolb.2022.918480

N/A

0DataRank · unranked

14 citations

David Ryoo, Marcella Orwick‐Rydmark, Athanasios Saragliadis, James C. Gumbart, Dirk Linke +1 more

Modeling intermediates of BamA folding an outer membrane protein

Biophysical Journal(2022)10.1016/j.bpj.2022.07.027

N/A

0DataRank · unranked

13 citations

David Ryoo, Karl Lundquist, James C. Gumbart, Katie M. Kuo

Structural Determinants of Indole-2-carboxamides: Identification of Lead Acetamides with Pan Antimycobacterial Activity

Journal of Medicinal Chemistry(2022)10.1021/acs.jmedchem.2c00352

N/A

0DataRank · unranked

14 citations

Pooja Hegde, Wei Li, Pavan Kumar Prathipati, Casey M. Stevens, Lixinhao Yang +14 more

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

Physical Chemistry Chemical Physics(2022)10.1039/d1cp05487b

N/A

0DataRank · unranked

4 citations

Oksana Gerlits, Luke L. Daemen, Ànna Pavlova, James C. Gumbart, Yongqiang Cheng +2 more

Conformational restriction shapes inhibition of a multidrug efflux adaptor protein

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.09.519754

N/A

0DataRank · unranked

1 citations

Muhammad Ramiz Uddin, Mohammad Moniruzzaman, Katie M. Kuo, A.J. Higgins, Laila M. N. Shah +7 more

N‐terminal Intrinsic Disorder of G Protein Gamma Subunits Is Important for Their Function as Governors of G Protein Signaling

The FASEB Journal(2022)10.1096/fasebj.2022.36.s1.r4185

N/A

0DataRank · unranked

0 citations

Wei Li, Yui Tik Pang, James C. Gumbart, Matthew P. Torres, Xinya Su

Structural basis of mitochondrial protein import by the TIM23 complex

Nature(2023)10.1038/s41586-023-06239-6

N/A

0DataRank · unranked

102 citations

Yuanyuan Chen, Diane L. Lynch, James C. Gumbart, Eunyong Park, Sue Sim

A Rigorous Framework for Calculating Protein–Protein Binding Affinities in Membranes

Journal of Chemical Theory and Computation(2023)10.1021/acs.jctc.3c00941

N/A

0DataRank · unranked

21 citations

James C. Gumbart, Haochuan Chen, Emad Tajkhorshid, Benoı̂t Roux, Christophe Chipot +1 more

Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein

Nature Communications(2023)10.1038/s41467-023-39615-x

N/A

0DataRank · unranked

27 citations

Muhammad Ramiz Uddin, Mohammad Moniruzzaman, Katie M. Kuo, A.J. Higgins, Laila M. N. Shah +7 more

Drug Binding to BamA Targets Its Lateral Gate

The Journal of Physical Chemistry B(2023)10.1021/acs.jpcb.3c04501

N/A

0DataRank · unranked

15 citations

Jinchan Liu, Anna Pavlova, James C. Gumbart, Katie M. Kuo

Insights into substrate transport and water permeation in the mycobacterial transporter MmpL3

Biophysical Journal(2023)10.1016/j.bpj.2023.03.018

N/A

0DataRank · unranked

14 citations

Atanu Acharya, Lixinhao Yang, Jinchan Liu, Emad Tajkhorshid, Helen I. Zgurskaya +3 more

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

PNAS Nexus(2023)10.1093/pnasnexus/pgad268

N/A

0DataRank · unranked

5 citations

Abigail M. Johnson, Zixing Fan, Lydia G Kenney, Manlin Xu, Ran Drori +5 more

Weak tension accelerates hybridization and dehybridization of short oligonucleotides

Nucleic Acids Research(2023)10.1093/nar/gkad118

N/A

0DataRank · unranked

4 citations

Jiyoun Jeong, James C. Gumbart, Harold D. Kim, Derek J. Hart

Uncovering the folding mechanism of pertactin: A comparative study of isolated and vectorial folding

Biophysical Journal(2023)10.1016/j.bpj.2023.03.021

N/A

0DataRank · unranked

5 citations

Anthony Hazel, James C. Gumbart, Yui Tik Pang

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

Journal of Biological Chemistry(2023)10.1016/j.jbc.2023.104947

N/A

0DataRank · unranked

3 citations

Yui Tik Pang, Wei Li, James C. Gumbart, Joshua B. Kelley, Matthew P. Torres +1 more

Competition between inside-out unfolding and pathogenic aggregation in an amyloid-forming β-propeller

Nature Communications(2024)10.1038/s41467-023-44479-2

N/A

0DataRank · unranked

13 citations

Mubark D. Mebrat, Hailee F. Scelsi, Minjoo Kim, Minh Thu, Xinya Su +8 more

From simple to complex: Reconstructing all-atom structures from coarse-grained models using cg2all

Structure(2024)10.1016/j.str.2023.12.004

N/A

0DataRank · unranked

8 citations

Lixinhao Yang, James C. Gumbart, Yui Tik Pang

Allosteric coupling of substrate binding and proton translocation in MmpL3 transporter from Mycobacterium tuberculosis

mBio(2024)10.1128/mbio.02183-24

N/A

0DataRank · unranked

8 citations

Wěi Li, Lixinhao Yang, Anna E. Grzegorzewicz, Mary Jackson, James C. Gumbart +2 more

Seeing is believing: Illuminating the Gram-negative outer membrane with molecular dynamics simulations

Current Opinion in Structural Biology(2024)10.1016/j.sbi.2024.102828

N/A

0DataRank · unranked

5 citations

Lixinhao Yang, James C. Gumbart, Gvantsa Gutishvili

Broadening access to small-molecule parameterization with the force field toolkit

The Journal of Chemical Physics(2024)10.1063/5.0196848

N/A

0DataRank · unranked

4 citations

Ànna Pavlova, P. Nelson, Zachary L. Glick, Lan Yang, Yui Tik Pang +6 more

SANS reveals lipid-dependent oligomerization of an intramembrane aspartyl protease from H. volcanii

Biophysical Journal(2024)10.1016/j.bpj.2024.05.029

N/A

0DataRank · unranked

3 citations

Yuqi Wu, Wellington Leite, Sai Venkatesh Pingali, Kevin L. Weiss, Arshay J. Grant +7 more

Generative β-hairpin design using a residue-based physicochemical property landscape

Biophysical Journal(2024)10.1016/j.bpj.2024.01.029

N/A

0DataRank · unranked

3 citations

Gemechis D. Degaga, Wei Li, Yui Tik Pang, Andrew C. McShan, James C. Gumbart +3 more

Thicket and Mesh: How the Outer Membrane Can Resist Tension Imposed by the Cell Wall

The Journal of Physical Chemistry B(2024)10.1021/acs.jpcb.3c08510

N/A

0DataRank · unranked

3 citations

Hyea Hwang, James C. Gumbart, David Ryoo

Substrate recognition mechanism of the endoplasmic reticulum-associated ubiquitin ligase Doa10

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.01.09.574907

N/A

0DataRank · unranked

1 citations

Samuel Itskanov, Diane L. Lynch, Yuanyuan Chen, Aasha Turner, James C. Gumbart +2 more

Mg 2+ -dependent mechanism of environmental versatility in a multidrug efflux pump

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.06.10.597921

N/A

0DataRank · unranked

1 citations

Muhammad Ramiz Uddin, Katie M. Kuo, Laila M. N. Shah, Nicola J. Harris, Paula J. Booth +5 more

Wild-type and single-O-antigen repeat outer-membrane vesicles induce equivalent protection against homologous and heterologous Salmonella challenge

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.07.03.601871

N/A

0DataRank · unranked

1 citations

Siân E. Jossi, Edith Marcial‐Juárez, Marisol Pérez-Toledo, Ruby Persaud, Anna E. Schager +16 more

Structural characterization of the POTRA domains from A. baumannii reveals new conformations in BamA

Structure(2024)10.1016/j.str.2024.08.013

N/A

0DataRank · unranked

0 citations

Robert E. Stephenson, Dante P. Ricci, Lixinhao Yang, James C. Gumbart, Nicholas Noinaj +1 more

Protein Structure Prediction in the 3D HP Model Using Deep Reinforcement Learning

arXiv (Cornell University)(2024)10.48550/arxiv.2412.20329

N/A

0DataRank · unranked

0 citations

Yui Tik Pang, James C. Gumbart, Giovanny Espitia

Using Machine Learning to Analyze Molecular Dynamics Simulations of Biomolecules

The Journal of Physical Chemistry B(2025)10.1021/acs.jpcb.4c08824

N/A

0DataRank · unranked

12 citations

Elisa Rheaume, Katie M. Kuo, Shina Caroline Lynn Kamerlin, James C. Gumbart, Alfie-Louise R. Brownless

Mg2+-dependent mechanism of environmental versatility in a multidrug efflux pump

Structure(2025)10.1016/j.str.2024.12.012

N/A

0DataRank · unranked

8 citations

Muhammad Ramiz Uddin, Katie M. Kuo, Laila M. N. Shah, Nicola J. Harris, Paula J. Booth +5 more

Machine Learning of Molecular Dynamics Simulations Provides Insights into the Modulation of Viral Capsid Assembly

Journal of Chemical Information and Modeling(2025)10.1021/acs.jcim.5c00274

N/A

0DataRank · unranked

8 citations

Zixing Fan, Diane L. Lynch, James C. Gumbart, Ànna Pavlova

Structural insights into outer membrane protein biogenesis in pathogenic Neisseria

Structure(2025)10.1016/j.str.2025.08.009

N/A

0DataRank · unranked

1 citations

Zixing Fan, Moloud Aflaki Sooreshjani, James C. Gumbart, Nicholas Noinaj, Evan Billings

The dynamic lateral gate of the mitochondrial β-barrel biogenesis machinery is blocked by darobactin A

Nature Communications(2025)10.1038/s41467-025-66417-0

N/A

0DataRank · unranked

1 citations

Istvan Botos, Scout Hayashi, Gvantsa Gutishvili, Vadim Kotov, Katie M. Kuo +10 more

Protein Structure Prediction in the 3D HP Model Using Deep Reinforcement Learning

Qeios(2025)10.32388/2o1wfi

N/A

0DataRank · unranked

1 citations

Yui Tik Pang, James C. Gumbart, Giovanny Espitia

Integrative Structure and Function of the Vibrio cholerae Competence Pilus Machine

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.10.14.680967

N/A

0DataRank · unranked

1 citations

Stefan Kreida, Lixinhao Yang, Abigail E. Teipen, Diane L. Lynch, Ankur B. Dalia +3 more

Machine learning of molecular dynamics simulations provides insights into modulation of viral capsid assembly

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.02.07.637202

N/A

0DataRank · unranked

0 citations

Zixing Fan, Diane L. Lynch, James C. Gumbart, Ànna Pavlova

Weighted Ensemble Simulations Reveal Novel Conformations and Modulator Effects in Hepatitis B Virus Capsid Assembly

Journal of Chemical Theory and Computation(2025)10.1021/acs.jctc.5c01197

N/A

0DataRank · unranked

0 citations

Anna Pavlova, Zixing Fan, James C. Gumbart, Diane L. Lynch

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

Chemical Science(2020)10.1039/d0sc04942e

N/A

0DataRank · unranked

59 citations

Diane L. Lynch, Isabella Daidone, Laura Zanetti‐Polzi, Micholas Dean Smith, Chris Chipot +14 more

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

eLife(2020)10.7554/elife.58100

N/A

0DataRank · unranked

28 citations

Istvan Botos, Zijian Zhang, Karl Lundquist, James C. Gumbart, Susan K. Buchanan +1 more

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

The Journal of Chemical Physics(2020)10.1063/5.0022802

N/A

0DataRank · unranked

19 citations

Ànna Pavlova, Emad Tajkhorshid, James C. Gumbart, Yui Tik Pang

BamA is required for autotransporter secretion

Biochimica et Biophysica Acta (BBA) - General Subjects(2020)10.1016/j.bbagen.2020.129581

N/A

0DataRank · unranked

11 citations

Marcella Orwick Rydmark, Yui Tik Pang, Karl Lundquist, Dirk Linke, James C. Gumbart +1 more

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

PLoS Computational Biology(2020)10.1371/journal.pcbi.1008355

N/A

0DataRank · unranked

40 citations

James C. Gumbart, Jinchan Liu

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

Biophysical Journal(2020)10.1016/j.bpj.2020.05.033

N/A

0DataRank · unranked

35 citations

Julia Stockmann, Léon Beyer, Till Rudack, Andreas Nabers, James C. Gumbart +3 more

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

ChemRxiv(2020)10.26434/chemrxiv.13200227

N/A

0DataRank · unranked

7 citations

Micholas Dean Smith, Chris Chipot, James C. Gumbart, Diane L. Lynch, Anna Pavlova +3 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.23.002527

N/A

0DataRank · unranked

4 citations

Leda Bassit, Bryan D. Cox, Maksym Korablyov, Chris Chipot, Kiran Verma +4 more

A Novel Approach to Simulating the Gating Transitions of Mechanosensitive Channels

Biophysical Journal(2020)10.1016/j.bpj.2020.12.004

N/A

0DataRank · unranked

0 citations

James C. Gumbart

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

ChemRxiv(2020)10.26434/chemrxiv.13200227.v1

N/A

0DataRank · unranked

0 citations

Micholas Dean Smith, Chris Chipot, James C. Gumbart, Diane L. Lynch, Anna Pavlova +3 more

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

Nature Communications(2021)10.1038/s41467-021-27449-4

N/A

0DataRank · unranked

75 citations

Jeremy Bakelar, Karl Lundquist, Zijian Zhang, Katie M. Kuo, David Ryoo +8 more