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Thomas E. Cheatham

Thomas E. Cheatham

D-Index & Metrics

Chemistry

D-Index
69
Citations
54308
World Ranking
6065
National Ranking
1843

Overview

Thomas E. Cheatham is affiliated with the University of Utah in the United States. Their research primarily falls within the broad field of Biochemistry, Genetics, and Molecular Biology, with a particular focus on Molecular Biology. They have contributed to a diverse set of topics including DNA and nucleic acid chemistry, RNA and protein synthesis mechanisms, scientific computing and data management, research data management practices, as well as protein structure and dynamics, and advanced biosensing and bioanalysis techniques.

The scientist's work also intersects with areas related to information systems and management, covering subjects such as big data and business intelligence alongside ecological studies to a lesser extent.

Thomas E. Cheatham has published extensively, with recent notable papers including:

  • AmberTools, 2023, Journal of Chemical Information and Modeling
  • Ethidium bromide interactions with DNA: an exploration of a classic DNA-ligand complex with unbiased molecular dynamics simulations, 2021, Nucleic Acids Research
  • Assessing the Current State of Amber Force Field Modifications for DNA2023 Edition, 2023, Journal of Chemical Theory and Computation
  • Peptoid Residues Make Diverse, Hyperstable Collagen Triple-Helices, 2021, Journal of the American Chemical Society
  • Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?, 2021, Biophysical Reviews

Frequent coauthors in their collaborative research include Rodrigo Galindo-Murillo, Dana Brunson, Patrick Schmitz, David A. Case, and Lauren Winkler. These collaborations have contributed to the diverse and interdisciplinary nature of their research output.

Thomas E. Cheatham has published in several scientific venues, prominently in:

  • Journal of Chemical Theory and Computation
  • Practice and Experience in Advanced Research Computing
  • Journal of Chemical Information and Modeling
  • The Journal of Physical Chemistry B
  • Journal of the American Chemical Society

Their research covers important topics such as:

  • DNA and Nucleic Acid Chemistry
  • RNA and protein synthesis mechanisms
  • Scientific Computing and Data Management
  • Research Data Management Practices
  • Protein Structure and Dynamics
  • Advanced biosensing and bioanalysis techniques
  • Big Data and Business Intelligence

Best Publications

  • The Amber biomolecular simulation programs

    David A. Case;Thomas E. Cheatham;Tom Darden;Holger Gohlke

  • PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

    Daniel R. Roe;Thomas E. Cheatham

  • Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models

    Peter A. Kollman;Irina Massova;Carolina Reyes;Bernd Kuhn

  • Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

    In Suk Joung;Thomas E. Cheatham

  • AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules

    David A. Pearlman;David A. Case;James W. Caldwell;Wilson S. Ross

  • Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers

    Alberto Pérez;Iván Marchán;Daniel Svozil;Daniel Svozil;Jiri Sponer;Jiri Sponer

  • Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices

    Jayashree Srinivasan;Thomas E. Cheatham;Piotr Cieplak;Peter A. Kollman

  • Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

    Marie Zgarbová;Michal Otyepka;Michal Otyepka;Jiří Šponer;Jiří Šponer;Arnošt Mládek

  • A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat.

    Thomas E. Cheatham;Piotr Cieplak;Peter A. Kollman

  • Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins

    T. E. Cheatham;J. L. Miller;T. Fox;T. A. Darden

  • Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms.

    Jianyin Shao;Stephen W. Tanner;Nephi Thompson;Thomas E. Cheatham

  • Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters

    In Suk Joung;Thomas E. Cheatham

  • Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

    Marie Zgarbová;Jiří Šponer;Jiří Šponer;Michal Otyepka;Thomas E. Cheatham

  • Assessing the Current State of Amber Force Field Modifications for DNA

    Rodrigo Galindo-Murillo;James C. Robertson;Marie Zgarbová;Jiří Šponer;Jiří Šponer

  • The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition

    Stephen C. Harvey;Robert K.-Z. Tan;Thomas E. Cheatham

  • Molecular dynamics simulation of nucleic acids.

    Thomas E. Cheatham;Peter A. Kollman

  • Molecular dynamics simulation of nucleic acids: successes, limitations, and promise.

    Thomas E. Cheatham;Matthew A. Young

  • Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins

    Pavel Banáš;Daniel Hollas;Marie Zgarbová;Petr Jurečka

  • Molecular dynamics simulations highlight the structural differences among DNA: DNA, RNA:RNA, and DNA:RNA hybrid duplexes

    Thomas E. Cheatham;Peter A. Kollman

  • A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

    Richard Lavery;Krystyna Zakrzewska;David Beveridge;Thomas C. Bishop

Frequent Co-Authors

Jiří Šponer
Jiří Šponer Masaryk University
Peter A. Kollman
Peter A. Kollman University of California, San Francisco
David A. Case
David A. Case Rutgers, The State University of New Jersey
Michal Otyepka
Michal Otyepka Palacký University, Olomouc
Petr Jurečka
Petr Jurečka Palacký University, Olomouc
Jaroslav Koča
Jaroslav Koča Central European Institute of Technology
Modesto Orozco
Modesto Orozco University of Barcelona
Geoffrey C. Fox
Geoffrey C. Fox University of Virginia
David L. Beveridge
David L. Beveridge Wesleyan University
Bernard R. Brooks
Bernard R. Brooks National Institutes of Health

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