Thomas E. Cheatham

Research interests

Publications

• Recent Developments in Amber Biomolecular Simulations

  Journal of Chemical Information and Modeling · 2025 · https://doi.org/10.1021/acs.jcim.5c01063

• AmberTools

  Journal of Chemical Information and Modeling · 2023 · https://doi.org/10.1021/acs.jcim.3c01153

• Amber 2021: Reference Manual

  Open Repository and Bibliography (University of Luxembourg) · 2021

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

  Journal of Chemical Theory and Computation · 2016 · 10.1021/acs.jctc.6b00186

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

  Journal of Chemical Theory and Computation · 2015 · 10.1021/acs.jctc.5b00716

• μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

  Nucleic Acids Research · 2014 · https://doi.org/10.1093/nar/gku855

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

  Journal of Chemical Theory and Computation · 2013 · https://doi.org/10.1021/ct400341p

• Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

  Journal of Chemical Theory and Computation · 2013 · 10.1021/ct400154j

• Reference Simulations of Noncanonical Nucleic Acids with Different χ Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA

  Journal of Chemical Theory and Computation · 2012 · https://doi.org/10.1021/ct300275s

• Quantum mechanically derived AMBER‐compatible heme parameters for various states of the cytochrome P450 catalytic cycle

  Journal of Computational Chemistry · 2011 · 10.1002/jcc.21922

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

  Journal of Chemical Theory and Computation · 2011 · 10.1021/ct200162x

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

  Journal of Chemical Theory and Computation · 2010 · 10.1021/ct100481h

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

  Nucleic Acids Research · 2009 · 10.1093/nar/gkp834

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

  The Journal of Physical Chemistry B · 2009 · 10.1021/jp902584c

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

  The Journal of Physical Chemistry B · 2008 · https://doi.org/10.1021/jp8001614

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

  Biophysical Journal · 2007 · 10.1529/biophysj.106.097782

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

  Journal of Chemical Theory and Computation · 2007 · 10.1021/ct700119m

• An accurate and simple quantum model for liquid water

  The Journal of Chemical Physics · 2006 · https://doi.org/10.1063/1.2386157

• The Amber biomolecular simulation programs

  Journal of Computational Chemistry · 2005 · https://doi.org/10.1002/jcc.20290

• Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. I. Research Design and Results on d(CpG) Steps

  Biophysical Journal · 2004 · 10.1529/biophysj.104.045252

• Molecular Dynamics Simulations and Thermodynamics Analysis of DNA−Drug Complexes. Minor Groove Binding between 4‘,6-Diamidino-2-phenylindole and DNA Duplexes in Solution

  Journal of the American Chemical Society · 2003 · https://doi.org/10.1021/ja025660d

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

  Biopolymers · 2000 · 10.1002/1097-0282(2000)56:4<232::aid-bip10037>3.0.co;2-h

• Molecular Dynamics Simulation of Nucleic Acids

  Annual Review of Physical Chemistry · 2000 · 10.1146/annurev.physchem.51.1.435

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

  Accounts of Chemical Research · 2000 · https://doi.org/10.1021/ar000033j

• A Modified Version of the Cornell et al. Force Field with Improved Sugar Pucker Phases and Helical Repeat

  Journal of Biomolecular Structure and Dynamics · 1999 · 10.1080/07391102.1999.10508297

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

  Journal of the American Chemical Society · 1998 · 10.1021/ja981844+

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

  Journal of Computational Chemistry · 1998 · 10.1002/(sici)1096-987x(199805)19:7<726::aid-jcc4>3.0.co;2-s

• 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

  Computer Physics Communications · 1995 · 10.1016/0010-4655(95)00041-d

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

  Journal of the American Chemical Society · 1995 · 10.1021/ja00119a045

Current projects

No projects listed.