Thomas E. Cheatham

51.6k total citations · 14 hit papers
185 papers, 39.1k citations indexed

About

Thomas E. Cheatham is a scholar working on Molecular Biology, Ecology and Information Systems. According to data from OpenAlex, Thomas E. Cheatham has authored 185 papers receiving a total of 39.1k indexed citations (citations by other indexed papers that have themselves been cited), including 120 papers in Molecular Biology, 22 papers in Ecology and 17 papers in Information Systems. Recurrent topics in Thomas E. Cheatham's work include DNA and Nucleic Acid Chemistry (91 papers), RNA and protein synthesis mechanisms (74 papers) and Protein Structure and Dynamics (38 papers). Thomas E. Cheatham is often cited by papers focused on DNA and Nucleic Acid Chemistry (91 papers), RNA and protein synthesis mechanisms (74 papers) and Protein Structure and Dynamics (38 papers). Thomas E. Cheatham collaborates with scholars based in United States, Czechia and Germany. Thomas E. Cheatham's co-authors include Daniel R. Roe, David A. Case, In Suk Joung, Peter A. Kollman, Jiřı́ Šponer, Tom Darden, Piotr Cieplak, Carlos Simmerling, Kenneth M. Merz and Alexey V. Onufriev and has published in prestigious journals such as Science, Proceedings of the National Academy of Sciences and Journal of the American Chemical Society.

In The Last Decade

Thomas E. Cheatham

178 papers receiving 38.7k citations

Hit Papers

The Amber biomolecular simulation programs 1995 2026 2005 2015 2005 2013 2000 2008 1995 2.5k 5.0k 7.5k
What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

  1. The Amber biomolecular simulation programs
    2005 7.5k citations Thomas E. Cheatham et al. profile →
  2. PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
    2013 5.4k citations Daniel R. Roe, Thomas E. Cheatham Journal of Chemical Theory and Computation profile →
  3. Calculating Structures and Free Energies of Complex Molecules:  Combining Molecular Mechanics and Continuum Models
    2000 4.0k citations Thomas E. Cheatham et al. profile →
  4. Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations
    2008 2.8k citations In Suk Joung, Thomas E. Cheatham The Journal of Physical Chemistry B profile →
  5. 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
    1995 2.7k citations Thomas E. Cheatham et al. profile →
  6. Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers
    2007 1.8k citations Jiřı́ Šponer, Thomas E. Cheatham et al. profile →
  7. Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices
    1998 1.4k citations Thomas E. Cheatham et al. Journal of the American Chemical Society profile →
  8. Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles
    2011 872 citations Marie Zgarbová, Michal Otyepka et al. Journal of Chemical Theory and Computation profile →
  9. A Modified Version of the Cornellet al.Force Field with Improved Sugar Pucker Phases and Helical Repeat
    1999 839 citations Thomas E. Cheatham et al. profile →
  10. Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins
    1995 717 citations Thomas E. Cheatham et al. Journal of the American Chemical Society profile →
  11. Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms
    2007 703 citations Thomas E. Cheatham et al. Journal of Chemical Theory and Computation profile →
  12. Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters
    2009 478 citations In Suk Joung, Thomas E. Cheatham The Journal of Physical Chemistry B profile →
  13. Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA
    2015 401 citations Marie Zgarbová, Jiřı́ Šponer et al. Journal of Chemical Theory and Computation profile →
  14. Assessing the Current State of Amber Force Field Modifications for DNA
    2016 397 citations Rodrigo Galindo‐Murillo, J.C. Robertson et al. Journal of Chemical Theory and Computation profile →

Peers — A (Enhanced Table)

Peers by citation overlap · career bar shows stage (early→late) cites · hero ref

Name h Career Trend Papers Cites
Thomas E. Cheatham United States 61 29.0k 4.9k 4.0k 3.6k 3.3k 185 39.1k
Piotr Cieplak United States 46 26.4k 0.9× 7.3k 1.5× 3.9k 1.0× 6.7k 1.9× 4.8k 1.5× 126 41.0k
Jeremy C. Smith United States 92 32.0k 1.1× 7.8k 1.6× 3.3k 0.8× 5.7k 1.6× 3.9k 1.2× 848 58.8k
Carlos Simmerling United States 43 20.9k 0.7× 5.3k 1.1× 3.6k 0.9× 2.6k 0.7× 2.5k 0.8× 106 28.3k
Darrin M. York United States 52 20.8k 0.7× 6.2k 1.3× 2.7k 0.7× 6.0k 1.7× 4.0k 1.2× 251 35.4k
Barry Honig United States 108 37.5k 1.3× 9.0k 1.8× 3.8k 1.0× 6.9k 1.9× 3.9k 1.2× 347 51.3k
Elaine C. Meng United States 29 32.3k 1.1× 4.9k 1.0× 4.1k 1.0× 1.2k 0.3× 4.4k 1.3× 35 50.0k
David E. Shaw United States 85 29.5k 1.0× 6.1k 1.2× 7.8k 1.9× 2.5k 0.7× 4.1k 1.3× 282 43.5k
Christopher I. Bayly United States 33 17.5k 0.6× 5.8k 1.2× 4.0k 1.0× 4.8k 1.3× 4.3k 1.3× 77 29.0k
Charles L. Brooks United States 94 29.7k 1.0× 10.4k 2.1× 3.7k 0.9× 8.1k 2.2× 2.7k 0.8× 427 40.5k
Alan E. Mark Australia 74 26.8k 0.9× 8.1k 1.6× 3.2k 0.8× 7.6k 2.1× 5.6k 1.7× 242 44.1k

Countries citing papers authored by Thomas E. Cheatham

Since Specialization
Citations

This map shows the geographic impact of Thomas E. Cheatham's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Thomas E. Cheatham with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Thomas E. Cheatham more than expected).

Fields of papers citing papers by Thomas E. Cheatham

Since Specialization
Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Thomas E. Cheatham. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Thomas E. Cheatham. The network helps show where Thomas E. Cheatham may publish in the future.

Co-authorship network of co-authors of Thomas E. Cheatham

This figure shows the co-authorship network connecting the top 25 collaborators of Thomas E. Cheatham. A scholar is included among the top collaborators of Thomas E. Cheatham based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Thomas E. Cheatham. Thomas E. Cheatham is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

20 of 20 papers shown
1.
Lima, Maria Carolina P., et al.. (2024). 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. 128(27). 6476–6491. 2 indexed citations
2.
Cheatham, Thomas E., et al.. (2024). The mechanism of covalent inhibition of LAR phosphatase by illudalic acid. Bioorganic & Medicinal Chemistry Letters. 104. 129740–129740. 1 indexed citations
3.
Winkler, Lauren, et al.. (2023). 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. 20(2). 625–643. 7 indexed citations
4.
Winkler, Lauren & Thomas E. Cheatham. (2023). Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide. Journal of Chemical Information and Modeling. 63(8). 2505–2511. 10 indexed citations
5.
Qin, Zhao, Helen H. Kang, Frank G. Whitby, et al.. (2021). Peptoid Residues Make Diverse, Hyperstable Collagen Triple-Helices. Journal of the American Chemical Society. 143(29). 10910–10919. 37 indexed citations
6.
Wang, Yuanxiang, Benjamin Bruno, Chen Diao, et al.. (2017). Application of Thiol–yne/Thiol–ene Reactions for Peptide and Protein Macrocyclizations. Chemistry - A European Journal. 23(29). 7087–7092. 43 indexed citations
7.
Zgarbová, Marie, Jiřı́ Šponer, Michal Otyepka, et al.. (2015). 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. 11(12). 5723–5736. 401 indexed citations breakdown →
8.
Bergonzo, Christina, Niel M. Henriksen, Daniel R. Roe, & Thomas E. Cheatham. (2015). Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields. RNA. 21(9). 1578–1590. 107 indexed citations
9.
Robertson, J.C. & Thomas E. Cheatham. (2015). DNA Backbone BI/BII Distribution and Dynamics in E2 Protein-Bound Environment Determined by Molecular Dynamics Simulations. The Journal of Physical Chemistry B. 119(44). 14111–14119. 10 indexed citations
10.
Roe, Daniel R. & Thomas E. Cheatham. (2013). PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data. Journal of Chemical Theory and Computation. 9(7). 3084–3095. 5423 indexed citations breakdown →
11.
Bergonzo, Christina, Niel M. Henriksen, Daniel R. Roe, et al.. (2013). Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide. Journal of Chemical Theory and Computation. 10(1). 492–499. 109 indexed citations
12.
Joung, In Suk, Özgül Persil Çetinkol, Nicholas V. Hud, & Thomas E. Cheatham. (2009). Molecular dynamics simulations and coupled nucleotide substitution experiments indicate the nature of A·A base pairing and a putative structure of the coralyne-induced homo-adenine duplex. Nucleic Acids Research. 37(22). 7715–7727. 27 indexed citations
13.
Cheatham, Thomas E., Amr F. Fahmy, & Dan Ştefănescu. (1994). Supporting multiple evolving compilers.. Software Engineering and Knowledge Engineering. 241–248. 3 indexed citations
14.
Cheatham, Thomas E., Amr F. Fahmy, & Dan Ştefănescu. (1994). H-BSP - A General Purpose Parallel Computing Environment.. IFIP Congress. 515–520. 2 indexed citations
15.
Cheatham, Thomas E. & Dan Ştefănescu. (1992). A Suite of Optimizers Based on Abstract Interpretation.. 75–81. 1 indexed citations
16.
Cheatham, Thomas E.. (1989). Process programming and process models. 49–51. 2 indexed citations
17.
Balzer, Robert, et al.. (1984). Software technology in the 1990's: using a new paradigm.. 3–9. 5 indexed citations
18.
Cheatham, Thomas E., et al.. (1981). Program refinement by transformation. International Conference on Software Engineering. 430–437. 29 indexed citations
19.
Cheatham, Thomas E., et al.. (1979). A system for program refinement. International Conference on Software Engineering. 53–62. 28 indexed citations
20.
Cheatham, Thomas E.. (1971). The Recent Evolution of Programming Languages.. IFIP Congress. 298–313. 10 indexed citations

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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