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T. Cheatham · SciRah

Researcher profile · Semantic Scholar

T. Cheatham

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T. Cheatham — researcher profile on SciRah

h-index: 64
Works: 183
Citations: 46K

Most-cited papers

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data.
D. Roe, T. Cheatham
2013Journal of Chemical Theory and Computation6,927 citations
Semantic Scholar
Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA.
Marie Zgarbová, J. Šponer, M. Otyepka, T. Cheatham +2 more
2015Journal of Chemical Theory and Computation490 citations
Semantic Scholar
Assessing the Current State of Amber Force Field Modifications for DNA
Rodrigo Galindo-Murillo, J. C. Robertson, Marie Zgarbová, J. Šponer +3 more
2016Journal of Chemical Theory and Computation477 citations Open access
Semantic Scholar
Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle
Kumars Shahrokh, A. Orendt, G. Yost, T. Cheatham
2011Journal of Computational Chemistry290 citations Open access
Semantic Scholar
Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters
Marie Zgarbová, F. Luque, J. Šponer, T. Cheatham +2 more
2013Journal of Chemical Theory and Computation257 citations Open access
Semantic Scholar
Recent Developments in Amber Biomolecular Simulations
David A. Case, D. Cerutti, Vinícius Wilian D Cruzeiro, Thomas A. Darden +27 more
2025Journal of Chemical Information and Modeling238 citations Open access
Semantic Scholar
Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA
Miroslav Krepl, Marie Zgarbová, Petr Stadlbauer, M. Otyepka +5 more
2012Journal of Chemical Theory and Computation236 citations Open access
Semantic Scholar
μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA
M. Pasi, J. Maddocks, D. Beveridge, T. Bishop +15 more
2014Nucleic Acids Research202 citations Open access
Semantic Scholar
Twenty-five years of nucleic acid simulations
T. Cheatham, D. Case
2013Biopolymers179 citations Open access
Semantic Scholar
Parallelization of CPPTRAJ Enables Large Scale Analysis of Molecular Dynamics Trajectory Data
D. Roe, T. Cheatham
2018Journal of Computational Chemistry176 citations Open access
Semantic Scholar
Intercalation processes of copper complexes in DNA
Rodrigo Galindo-Murillo, J. García-Ramos, L. Ruiz-Azuara, T. Cheatham +1 more
2015Nucleic Acids Research162 citations Open access
Semantic Scholar
Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)
Rodrigo Galindo-Murillo, D. Roe, T. Cheatham
2014Biochimica et Biophysica Acta158 citations Open access
Semantic Scholar
Improved Force Field Parameters Lead to a Better Description of RNA Structure.
Christina Bergonzo, T. Cheatham
2015Journal of Chemical Theory and Computation156 citations
Semantic Scholar
Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields
Christina Bergonzo, N. M. Henriksen, D. Roe, T. Cheatham
2015RNA: A publication of the RNA Society136 citations Open access
Semantic Scholar
Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide
Christina Bergonzo, N. M. Henriksen, D. Roe, Jason M. Swails +2 more
2013Journal of Chemical Theory and Computation123 citations Open access
Semantic Scholar
Ethidium bromide interactions with DNA: an exploration of a classic DNA–ligand complex with unbiased molecular dynamics simulations
Rodrigo Galindo-Murillo, T. Cheatham
2021Nucleic Acids Research121 citations Open access
Semantic Scholar
Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures
J. Šponer, Xiaohui Cang, T. Cheatham
2012Methods120 citations Open access
Semantic Scholar
Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations
J. Šponer, Arnošt Mládek, N. Špačková, Xiaohui Cang +2 more
2013Journal of the American Chemical Society108 citations Open access
Semantic Scholar
Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations
Petr Stadlbauer, Miroslav Krepl, T. Cheatham, J. Koča +1 more
2013Nucleic Acids Research102 citations Open access
Semantic Scholar
Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics with Hamiltonian Replica Exchange Methods
D. Roe, Christina Bergonzo, T. Cheatham
2014Journal of Physical Chemistry B99 citations Open access
Semantic Scholar
The need to implement FAIR principles in biomolecular simulations
R. Amaro, J. Åqvist, Ivet Bahar, F. Battistini +125 more
2024Nature Methods80 citations Open access
Semantic Scholar
On the absence of intra-helical DNA dynamics on the µs to ms timescale
Rodrigo Galindo-Murillo, D. Roe, T. Cheatham
2014Nature Communications78 citations Open access
Semantic Scholar
Self-tensioning aquatic caddisfly silk: Ca2+-dependent structure, strength, and load cycle hysteresis.
Nicholas N. Ashton, D. Roe, R. Weiss, T. Cheatham +1 more
2013Biomacromolecules72 citations
Semantic Scholar
Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations.
Petr Stadlbauer, L. Trantírek, T. Cheatham, J. Koča +1 more
2014Biochimie71 citations Open access
Semantic Scholar
Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations
N. M. Henriksen, D. Roe, T. Cheatham
2013Journal of Physical Chemistry B61 citations Open access
Semantic Scholar
Assessing the Current State of Amber Force Field Modifications for DNA—2023 Edition
Olivia Love, Rodrigo Galindo-Murillo, Marie Zgarbová, J. Šponer +2 more
2023Journal of Chemical Theory and Computation59 citations Open access
Semantic Scholar
Molecular basis for the broad substrate selectivity of a peptide prenyltransferase
Y. Hao, Elizabeth Pierce, D. Roe, M. Morita +5 more
2016Proceedings of the National Academy of Sciences of the United States of America54 citations Open access
Semantic Scholar
Transitions of Double-Stranded DNA Between the A- and B-Forms
James T. Waters, Xiang-Jun Lu, Rodrigo Galindo-Murillo, J. Gumbart +3 more
2016Journal of Physical Chemistry B48 citations Open access
Semantic Scholar
Peptoid Residues Make Diverse, Hyperstable Collagen Triple-Helices
J. Kessler, Grace Kang, Z. Qin, Helen H. Kang +5 more
2020Journal of the American Chemical Society42 citations Open access
Semantic Scholar
Application of Thiol-yne/Thiol-ene Reactions for Peptide and Protein Macrocyclizations.
Yuan-Xiang Wang, Benjamin J. Bruno, Sean P Cornillie, Jason M. Nogieira +4 more
2017Chemistry40 citations
Semantic Scholar
Efficient treatment of induced dipoles.
Andrew C. Simmonett, Frank C. Pickard, Yihan Shao, T. Cheatham +1 more
2015Journal of Chemical Physics40 citations Open access
Semantic Scholar
Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?
Gabriela da Rosa, Leandro Grille, Victoria Calzada, Katya Ahmad +22 more
2021Biophysical Reviews39 citations Open access
Semantic Scholar
Amber 2015, University of California, San Francisco
D. Case, J. Berryman, Robin M. Betz, D. Cerutti +36 more
201538 citations
Semantic Scholar
Totopotensamides, Polyketide-Cyclic Peptide Hybrids from a Mollusk-Associated Bacterium Streptomyces sp
Zhen-Jian Lin, Malem S. Flores, Imelda Forteza, N. M. Henriksen +7 more
2012Journal of Natural Products33 citations Open access
Semantic Scholar
Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences
Marie Zgarbová, P. Jurečka, F. Lankaš, T. Cheatham +2 more
2017Journal of Chemical Information and Modeling32 citations Open access
Semantic Scholar
The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis
T. Cheatham, D. Roe
2015Computing in science & engineering (Print)32 citations
Semantic Scholar
Oxazinin A, a Pseudodimeric Natural Product of Mixed Biosynthetic Origin from a Filamentous Fungus
Zhen-Jian Lin, Michael Koch, M. A. Abdel Aziz, Rodrigo Galindo-Murillo +5 more
2014Organic Letters31 citations Open access
Semantic Scholar
Araiosamines A–D: Tris-bromoindole Cyclic Guanidine Alkaloids from the Marine Sponge Clathria (Thalysias) araiosa
Xiaomei Wei, N. M. Henriksen, J. Skalicky, M. K. Harper +3 more
2011Journal of Organic Chemistry31 citations Open access
Semantic Scholar
Conformational dynamics of CYP3A4 demonstrate the important role of Arg212 coupled with the opening of ingress, egress and solvent channels to dehydrogenation of 4-hydroxy-tamoxifen
Kiumars Shahrokh, T. Cheatham, G. Yost
2012Biochimica et Biophysica Acta29 citations Open access
Semantic Scholar
Journal of Biomolecular Structure and Dynamics: Editorial Board
R. Sarma, E. Bichenkova, T. Cheatham, V. Makeev +9 more
201327 citations
Semantic Scholar
Computational DNA binding studies of (–)-epigallocatechin-3-gallate
Rodrigo Galindo-Murillo, T. Cheatham
2018Journal of Biomolecular Structure and Dynamics26 citations Open access
Semantic Scholar
Consensus Conformations of Dinucleoside Monophosphates Described with Well-Converged Molecular Dynamics Simulations.
Hamed S. Hayatshahi, N. M. Henriksen, T. Cheatham
2018Journal of Chemical Theory and Computation26 citations
Semantic Scholar
Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure
N. M. Henriksen, D. R. Davis, T. Cheatham
2012Journal of Biomolecular NMR26 citations Open access
Semantic Scholar
Evaluating the accuracy of the AMBER protein force fields in modeling dihydrofolate reductase structures: misbalance in the conformational arrangements of the flexible loop domains
Olivia Love, M. C. P. Lima, C. Clark, Sean P Cornillie +2 more
2022Journal of Biomolecular Structure and Dynamics25 citations Open access
Semantic Scholar
Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg2+ Bound Structure in the Presence of Monovalent Ions
Christina Bergonzo, K. Hall, T. Cheatham
2015Journal of Physical Chemistry B23 citations Open access
Semantic Scholar
iBIOMES: Managing and sharing biomolecular simulation data in a distributed environment
J. Thibault, J. Facelli, T. Cheatham
2013Journal of Chemical Information and Modeling23 citations Open access
Semantic Scholar
modXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields
Olivia Love, Rodrigo Galindo-Murillo, Daniel R. Roe, P. Dans +2 more
2024Journal of Chemical Theory and Computation21 citations Open access
Semantic Scholar
DNA Binding Dynamics and Energetics of Cobalt, Nickel, and Copper Metallopeptides
Rodrigo Galindo-Murillo, T. Cheatham
2014ChemMedChem19 citations
Semantic Scholar
Task-parallel Analysis of Molecular Dynamics Trajectories
Ioannis Paraskevakos, André Luckow, Mahzad Khoshlessan, George Chantzialexiou +4 more
2018International Conference on Parallel Processing17 citations Open access
Semantic Scholar
Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations
Z. Heidari, D. Roe, Rodrigo Galindo-Murillo, Jahan B. Ghasemi +1 more
2016Journal of Chemical Information and Modeling17 citations Open access
Semantic Scholar

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J. Šponer×12
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Marie Zgarbová

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