Thomas E. Cheatham

Also affiliated with Medicina

Biochemistry, Genetics and Molecular BiologyComputer 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 17 papers. Top paper: “AmberTools”.

AmberTools

Journal of Chemical Information and Modeling(2023)10.1021/acs.jcim.3c01153

N/A

8.3DataRank · unranked

1950 citations

Hasan Metin Aktulga, Kellon Belfon, David S. Cerutti, G. Andrés Cisneros, Vinícius Wilian D. Cruzeiro +42 more

The Amber biomolecular simulation programs

Journal of Computational Chemistry(2005)10.1002/jcc.20290

N/A

1.4DataRank · unranked

9524 citations

Thomas E. Cheatham, Tom Darden, Holger Gohlke, Ray Luo, Kenneth M. Merz +6 more

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

Journal of Chemical Theory and Computation(2013)10.1021/ct400341p

N/A

1.3DataRank · unranked

7429 citations

Thomas E. Cheatham, Daniel R. Roe

Assessing the Current State of Amber Force Field Modifications for DNA─2023 Edition

Journal of Chemical Theory and Computation(2023)10.1021/acs.jctc.3c00233

N/A

0.635DataRank · unranked

68 citations

Rodrigo Galindo‐Murillo, Marie Zgarbová, Jiřı́ Šponer, Petr Jurečka, Thomas E. Cheatham +1 more

Ancillary Ligand in Ternary CuIIComplexes Guides Binding Selectivity toward Minor-Groove DNA

The Journal of Physical Chemistry B(2020)10.1021/acs.jpcb.0c09296

N/A

0.416DataRank · unranked

15 citations

Lauren Winkler, Juan Carlos García‐Ramos, Lena Ruíz-Azuara, Fernando Cortés‐Guzmán, Thomas E. Cheatham +1 more

Assessment of A- to B- DNA Transitions Utilizing the Drude Polarizable Force Field

Journal of Chemical Theory and Computation(2023)10.1021/acs.jctc.3c01002

N/A

0.385DataRank · unranked

12 citations

Rodrigo Galindo‐Murillo, Thomas E. Cheatham, Lauren Winkler

Application of Computed FTIR Spectra of Nucleotide Monophosphates to RNA Force Field Refinement

Journal of Chemical Theory and Computation(2025)10.1021/acs.jctc.5c00712

N/A

0.104DataRank · unranked

1 citations

Nathan D. Levinzon, Thomas E. Cheatham, Holly Freedman

The mechanism of covalent inhibition of LAR phosphatase by illudalic acid

Bioorganic & Medicinal Chemistry Letters(2024)10.1016/j.bmcl.2024.129740

N/A

0.104DataRank · unranked

1 citations

Nicole J. Rueb, Nathan D. Levinzon, Thomas E. Cheatham, Robert S. Gaston, Kh Tanvir Ahmed +5 more

Computational Modeling of Stapled Coiled-Coil Inhibitors Against Bcr-Abl: Toward a Treatment Strategy for CML

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.15.566894

N/A

0DataRank · unranked

2 citations

Braxten D. Hornsby, Carol S. Lim, Thomas E. Cheatham, Maria Carolina P. Lima

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

Journal of Chemical Theory and Computation(2024)10.1021/acs.jctc.4c01164

N/A

0DataRank · unranked

14 citations

Rodrigo Galindo‐Murillo, Daniel R. Roe, Pablo D. Dans, Thomas E. Cheatham, Christina Bergonzo +1 more

Recent Developments in Amber Biomolecular Simulations

Journal of Chemical Information and Modeling(2025)10.1021/acs.jcim.5c01063

N/A

0DataRank · unranked

131 citations

David S. Cerutti, Vinícius Wilian D. Cruzeiro, Thomas A. Darden, Robert E. Duke, Mahdieh Ghazimirsaeed +26 more

Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16

Proteins Structure Function and Bioinformatics(2025)10.1002/prot.70079

N/A

0DataRank · unranked

1 citations

Elisa Posani, Eugene F. Baulin, Janusz M. Bujnicki, Giovanni Bussi, Thomas E. Cheatham +46 more

Peptoid Residues Make Diverse, Hyperstable Collagen Triple Helices

ChemRxiv(2020)10.26434/chemrxiv.12921995

N/A

0DataRank · unranked

0 citations

Grace Kang, Zhao Qin, Helen H. Kang, Frank G. Whitby, Thomas E. Cheatham +4 more

Blind prediction of complex water and ion ensembles around RNA in CASP16

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.11.03.685595

N/A

0DataRank · unranked

0 citations

Elisa Posani, Eugene F. Baulin, Janusz M. Bujnicki, Giovanni Bussi, Thomas E. Cheatham +46 more

Ethidium bromide interactions with DNA: an exploration of a classic DNA–ligand complex with unbiased molecular dynamics simulations

Nucleic Acids Research(2021)10.1093/nar/gkab143

N/A

0DataRank · unranked

140 citations

Thomas E. Cheatham, Rodrigo Galindo‐Murillo

Peptoid Residues Make Diverse, Hyperstable Collagen Triple-Helices

Journal of the American Chemical Society(2021)10.1021/jacs.1c00708

N/A

0DataRank · unranked

47 citations

Grace Kang, Zhao Qin, Helen H. Kang, Frank G. Whitby, Thomas E. Cheatham +4 more

Peptoid Residues Make Diverse, Hyperstable Collagen Triple Helices

ChemRxiv(2020)10.26434/chemrxiv.12921995.v1

N/A

0DataRank · unranked

1 citations

Grace Kang, Zhao Qin, Helen H. Kang, Frank G. Whitby, Thomas E. Cheatham +4 more