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University of Utah: Salt Lake City, UT, US

2000-01-01 to present | Professor / Director (Medicinal Chemistry / CHPC)
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Thomas Cheatham

Works (25)

modXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields

Journal of Chemical Theory and Computation
2024-11-12 | Journal article
DOI: 10.1021/acs.jctc.4c01164
Contributors: Olivia Love; Rodrigo Galindo-Murillo; Daniel R. Roe; Pablo D. Dans; Thomas E. Cheatham III; Christina Bergonzo
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Molecular Modeling of Single- and Double-Hydrocarbon-Stapled Coiled-Coil Inhibitors against Bcr-Abl: Toward a Treatment Strategy for CML

The Journal of Physical Chemistry B
2024-07-11 | Journal article
DOI: 10.1021/acs.jpcb.4c02699
Contributors: Maria Carolina P. Lima; Braxten D. Hornsby; Carol S. Lim; Thomas E. Cheatham, III
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Crossref

van der Waals Parameter Scanning with Amber Nucleic Acid Force Fields: Revisiting Means to Better Capture the RNA/DNA Structure through MD

Journal of Chemical Theory and Computation
2024-01-23 | Journal article
DOI: 10.1021/acs.jctc.3c01164
Contributors: Olivia Love; Lauren Winkler; Thomas E. Cheatham, III
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Assessment of A- to B- DNA Transitions Utilizing the Drude Polarizable Force Field

Journal of Chemical Theory and Computation
2023-12-12 | Journal article
DOI: 10.1021/acs.jctc.3c01002
Contributors: Lauren Winkler; Rodrigo Galindo-Murillo; Thomas E. Cheatham, III
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Evaluating the accuracy of the AMBER protein force fields in modeling dihydrofolate reductase structures: misbalance in the conformational arrangements of the flexible loop domains

Journal of Biomolecular Structure and Dynamics
2023-09-02 | Journal article
DOI: 10.1080/07391102.2022.2098823
Contributors: Olivia Love; Maria Carolina Pacheco Lima; Casey Clark; Sean Cornillie; Shelly Roalstad; Thomas E. Cheatham III
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Crossref

Professionalization of Research Computing and Data: An Expanded Agenda

2023-07-23 | Conference paper
DOI: 10.1145/3569951.3593610
Contributors: Joel Cutcher-Gershenfeld; Torey Battelle; Dana Brunson; Thomas Cheatham; Jacob Fosso Tande; Douglas Jennewein; Julie Ma; Lauren A. Michael; Timothy Middelkoop; Henry Neeman et al.
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Assessing the Current State of Amber Force Field Modifications for DNA─2023 Edition

Journal of Chemical Theory and Computation
2023-07-11 | Journal article
DOI: 10.1021/acs.jctc.3c00233
Contributors: Olivia Love; Rodrigo Galindo-Murillo; Marie Zgarbová; Jiří Šponer; Petr Jurečka; Thomas E. Cheatham, III
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Crossref

Structures and Dynamics of DNA Mini-Dumbbells Are Force Field Dependent

Journal of Chemical Theory and Computation
2023-04-25 | Journal article
DOI: 10.1021/acs.jctc.3c00130
Contributors: Lauren Winkler; Rodrigo Galindo-Murillo; Thomas E. Cheatham, III
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Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide

Journal of Chemical Information and Modeling
2023-04-24 | Journal article
DOI: 10.1021/acs.jcim.3c00250
Contributors: Lauren Winkler; Thomas E. Cheatham, III
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Systematic Investigation of Tether Length and Phosphorus Configuration in Backbone Constrained Macrocyclic Nucleic Acids to Modulate Binding Kinetics for RNA

The Journal of Organic Chemistry
2023-03-17 | Journal article
DOI: 10.1021/acs.joc.2c02796
Contributors: Tamilselvan Rajasekaran; Graeme C. Freestone; Rodrigo Galindo-Murillo; Barbara Lugato; Hans Gaus; Michael T. Migawa; Eric. E. Swayze; Thomas E. Cheatham, III; Punit P. Seth; Stephen Hanessian
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Transient Hoogsteen Base Pairs Observed in Unbiased Molecular Dynamics Simulations of DNA

The Journal of Physical Chemistry Letters
2022-07-14 | Journal article
DOI: 10.1021/acs.jpclett.2c01348
Contributors: Rodrigo Galindo-Murillo; Thomas E. Cheatham, III
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Riboflavin Stabilizes Abasic, Oxidized G-Quadruplex Structures

Biochemistry
2022-02-15 | Journal article
DOI: 10.1021/acs.biochem.1c00598
Contributors: Rodrigo Galindo-Murillo; Lauren Winkler; Jingwei Ma; Fatjon Hanelli; Aaron M. Fleming; Cynthia J. Burrows; Thomas E. Cheatham, III
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Backbone Hydrocarbon-Constrained Nucleic Acids Modulate Hybridization Kinetics for RNA

Journal of the American Chemical Society
2022-02-02 | Journal article
DOI: 10.1021/jacs.1c12323
Contributors: Tamilselvan Rajasekaran; Graeme C. Freestone; Rodrigo Galindo-Murillo; Barbara Lugato; Lorena Rico; Juan C. Salinas; Hans Gaus; Michael T. Migawa; Eric E. Swayze; Thomas E. Cheatham, III et al.
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Advancing the Workforce That Supports Computationally and Data Intensive Research

Computing in Science & Engineering
2021-09-01 | Journal article
DOI: 10.1109/MCSE.2021.3098421
Contributors: Patrick Schmitz; Scott Yockel; Claire Mizumoto; Thomas Cheatham; Dana Brunson
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Peptoid Residues Make Diverse, Hyperstable Collagen Triple-Helices

Journal of the American Chemical Society
2021-07-28 | Journal article
DOI: 10.1021/jacs.1c00708
Contributors: Julian L. Kessler; Grace Kang; Zhao Qin; Helen Kang; Frank G. Whitby; Thomas E. Cheatham, III; Christopher P. Hill; Yang Li; S. Michael Yu
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Ancillary Ligand in Ternary CuII Complexes Guides Binding Selectivity toward Minor-Groove DNA

The Journal of Physical Chemistry B
2020-12-24 | Journal article
DOI: 10.1021/acs.jpcb.0c09296
Contributors: Rodrigo Galindo-Murillo; Lauren Winkler; Juan Carlos García-Ramos; Lena Ruiz-Azuara; Fernando Cortés-Guzmán; Thomas E. Cheatham, III
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Lessons learned in atomistic simulation of double-stranded DNA: Solvation and salt concerns [Article v1.0]

Living Journal of Computational Molecular Science
2019 | Journal article
DOI: 10.33011/livecoms.1.2.9974
Contributors: Rodrigo Galindo-Murillo; Thomas E. Cheatham III
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Exploring potentially alternative non-canonical DNA duplex structures through simulation

Journal of Biomolecular Structure and Dynamics
2019-06-13 | Journal article
DOI: 10.1080/07391102.2018.1483839
Contributors: Rodrigo Galindo-Murillo; Thomas E. Cheatham, III; Robert C. Hopkins
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Computational DNA binding studies of (–)-epigallocatechin-3-gallate

Journal of Biomolecular Structure and Dynamics
2018-10-03 | Journal article
DOI: 10.1080/07391102.2017.1389306
Contributors: Rodrigo Galindo-Murillo; Thomas E. Cheatham, III
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Computational Modeling of Stapled Peptides toward a Treatment Strategy for CML and Broader Implications in the Design of Lengthy Peptide Therapeutics

The Journal of Physical Chemistry B
2018-04-12 | Journal article
DOI: 10.1021/acs.jpcb.8b01014
Contributors: Sean P. Cornillie; Benjamin J. Bruno; Carol S. Lim; Thomas E. Cheatham, III
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Consensus Conformations of Dinucleoside Monophosphates Described with Well-Converged Molecular Dynamics Simulations

Journal of Chemical Theory and Computation
2018-03-13 | Journal article
DOI: 10.1021/acs.jctc.7b00581
Contributors: Hamed S. Hayatshahi; Niel M. Henriksen; Thomas E. Cheatham, III
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Investigating the ion dependence of the first unfolding step of GTPase-Associating Center ribosomal RNA

Journal of Biomolecular Structure and Dynamics
2018-01-02 | Journal article
DOI: 10.1080/07391102.2016.1274272
Contributors: Hamed S. Hayatshahi; Christina Bergonzo; Thomas E. Cheatham III
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Dissociative reactions of benzonorbornadienes with tetrazines: scope of leaving groups and mechanistic insights

Organic & Biomolecular Chemistry
2017 | Journal article
DOI: 10.1039/C7OB02191G
Contributors: M. Xu; R. Galindo-Murillo; T. E. Cheatham; R. M. Franzini
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Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences

Journal of Chemical Information and Modeling
2017-02-27 | Journal article
DOI: 10.1021/acs.jcim.6b00621
Contributors: Marie Zgarbová; Petr Jurečka; Filip Lankaš; Thomas E. Cheatham, III; Jiří Šponer; Michal Otyepka
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Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in GTPase-Associating Center RNA

The Journal of Physical Chemistry B
2017-01-26 | Journal article
DOI: 10.1021/acs.jpcb.6b08764
Contributors: Hamed S. Hayatshahi; Daniel R. Roe; Rodrigo Galindo-Murillo; Kathleen B. Hall; Thomas E. Cheatham, III
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Peer review (23 reviews for 7 publications/grants)

Review activity for ACS omega. (1)
Review activity for Biochemistry. (1)
Review activity for Journal of chemical information and modeling. (6)
Review activity for Journal of chemical theory and computation : (6)
Review activity for Journal of the American Chemical Society. (1)
Review activity for The journal of physical chemistry letters. (1)
Review activity for The journal of physical chemistry. (7)
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