Daniel R. Roe

12.4k total citations · 1 hit paper
38 papers, 7.7k citations indexed

About

Daniel R. Roe is a scholar working on Molecular Biology, Spectroscopy and Materials Chemistry. According to data from OpenAlex, Daniel R. Roe has authored 38 papers receiving a total of 7.7k indexed citations (citations by other indexed papers that have themselves been cited), including 30 papers in Molecular Biology, 8 papers in Spectroscopy and 8 papers in Materials Chemistry. Recurrent topics in Daniel R. Roe's work include Protein Structure and Dynamics (18 papers), DNA and Nucleic Acid Chemistry (11 papers) and RNA and protein synthesis mechanisms (9 papers). Daniel R. Roe is often cited by papers focused on Protein Structure and Dynamics (18 papers), DNA and Nucleic Acid Chemistry (11 papers) and RNA and protein synthesis mechanisms (9 papers). Daniel R. Roe collaborates with scholars based in United States, Netherlands and Iran. Daniel R. Roe's co-authors include Thomas E. Cheatham, Carlos Simmerling, Thi Hong Hai Nguyen, Christina Bergonzo, Rodrigo Galindo‐Murillo, Niel M. Henriksen, David A. Case, Viktor Horn̆ák, Richard A. Messerly and Edward J. Maginn and has published in prestigious journals such as Proceedings of the National Academy of Sciences, Nature Communications and The Journal of Chemical Physics.

In The Last Decade

Daniel R. Roe

35 papers receiving 7.7k citations

Hit Papers

align trajectories

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.

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 →

Peers — A (Enhanced Table)

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

Name	h						Papers	Cites
Daniel R. Roe United States	20	5.4k	1.1k	1.1k	766	559	38	7.7k
Lauren Wickstrom United States	17	6.3k 1.2×	1.3k 1.3×	1.3k 1.2×	817 1.1×	617 1.1×	23	8.8k
Lillian T. Chong United States	24	4.6k 0.8×	880 0.8×	1.2k 1.1×	615 0.8×	470 0.8×	58	6.3k
Koushik Kasavajhala United States	7	6.7k 1.2×	1.3k 1.2×	1.4k 1.3×	900 1.2×	582 1.0×	9	9.4k
Kevin Hauser United States	9	5.9k 1.1×	1.1k 1.0×	1.2k 1.2×	771 1.0×	477 0.9×	13	8.6k
Huafeng Xu United States	27	4.9k 0.9×	992 0.9×	1.5k 1.4×	743 1.0×	724 1.3×	63	7.5k
Yifei Qi United States	28	6.0k 1.1×	680 0.6×	807 0.8×	652 0.9×	472 0.8×	70	8.1k
Jens Erik Nielsen Ireland	31	6.9k 1.3×	1.6k 1.5×	941 0.9×	713 0.9×	394 0.7×	62	9.6k
Jason Swails United States	15	7.2k 1.3×	1.5k 1.4×	1.6k 1.5×	989 1.3×	717 1.3×	19	10.3k
Chun Wu United States	35	5.6k 1.0×	1.4k 1.3×	788 0.7×	559 0.7×	873 1.6×	114	8.0k
Noel Southall United States	48	4.1k 0.8×	675 0.6×	1.1k 1.0×	921 1.2×	433 0.8×	189	8.6k

Countries citing papers authored by Daniel R. Roe

Since Specialization

Citations

This map shows the geographic impact of Daniel R. Roe'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 Daniel R. Roe with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Daniel R. Roe more than expected).

Fields of papers citing papers by Daniel R. Roe

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Daniel R. Roe. 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 Daniel R. Roe. The network helps show where Daniel R. Roe may publish in the future.

Co-authorship network of co-authors of Daniel R. Roe

This figure shows the co-authorship network connecting the top 25 collaborators of Daniel R. Roe. A scholar is included among the top collaborators of Daniel R. Roe 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 Daniel R. Roe. Daniel R. Roe is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

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20 of 20 papers shown

Smith, Micah J., et al.. (2025). Extended Quality (eQual): Radial Threshold Clustering Based on n -ary Similarity. Journal of Chemical Information and Modeling. 65(10). 5062–5070.

Roe, Daniel R., et al.. (2025). CADENCE: Clustering Algorithm─Density-Based Exploration and Novelty Clustering with Efficiency. Journal of Chemical Information and Modeling. 65(13). 6968–6975.

Waibl, Franz, Monica L. Fernández‐Quintero, Steven Ramsey, et al.. (2025). Quantifying Spatially Resolved Hydration Thermodynamics Using Grid Inhomogeneous Solvation Theory [v1.0]. 6(1). 3059–3059.

Galindo‐Murillo, Rodrigo, et al.. (2024). modXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields. Journal of Chemical Theory and Computation. 20(21). 9354–9363. 4 indexed citations

Chen, Lieyang, Anthony Cruz, Daniel R. Roe, et al.. (2021). Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory. Journal of Chemical Theory and Computation. 17(5). 2714–2724. 25 indexed citations

Roe, Daniel R. & Bernard R. Brooks. (2021). Improving the speed of volumetric density map generation via cubic spline interpolation. Journal of Molecular Graphics and Modelling. 104. 107832–107832. 6 indexed citations

Grossfield, Alan, Paul N. Patrone, Daniel R. Roe, et al.. (2018). Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations. 1(1). 4 indexed citations

Maginn, Edward J., et al.. (2018). Best Practices for Computing Transport Properties 1. Self-Diffusivity and Viscosity from Equilibrium Molecular Dynamics [Article v1.0]. 1(1). 6324–6324. 211 indexed citations

Grossfield, Alan, Paul N. Patrone, Daniel R. Roe, et al.. (2018). Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1.0]. PubMed. 1(1). 117 indexed citations

10.

Nguyen, Thi Hong Hai, Daniel R. Roe, Jason Swails, & David A. Case. (2016). PYTRAJ v1.0.0.dev1: Interactive data analysis for molecular dynamics simulations. Zenodo (CERN European Organization for Nuclear Research). 17 indexed citations

11.

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

12.

Thibault, Julien, Daniel R. Roe, Karen Eilbeck, Thomas E. Cheatham, & Julio C. Facelli. (2015). Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology. SAR and QSAR in environmental research. 26(7-9). 577–593. 2 indexed citations

13.

Galindo‐Murillo, Rodrigo, Daniel R. Roe, & Thomas E. Cheatham. (2014). Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC). Biochimica et Biophysica Acta (BBA) - General Subjects. 1850(5). 1041–1058. 136 indexed citations

14.

Thibault, Julien, Daniel R. Roe, Julio C. Facelli, & Thomas E. Cheatham. (2014). Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing. Journal of Cheminformatics. 6(1). 4–4. 12 indexed citations

15.

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 →

16.

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

17.

Nguyen, Thi Hong Hai, Daniel R. Roe, & Carlos Simmerling. (2013). Improved Generalized Born Solvent Model Parameters for Protein Simulations. Journal of Chemical Theory and Computation. 9(4). 2020–2034. 403 indexed citations

18.

Brozell, Scott R., Sudipto Mukherjee, Trent E. Balius, et al.. (2012). Evaluation of DOCK 6 as a pose generation and database enrichment tool. Journal of Computer-Aided Molecular Design. 26(6). 749–773. 130 indexed citations

19.

Luchko, Tyler, Sergey Gusarov, Daniel R. Roe, et al.. (2010). Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber. Journal of Chemical Theory and Computation. 6(3). 607–624. 209 indexed citations

20.

Roe, Daniel R., Viktor Horn̆ák, & Carlos Simmerling. (2005). Folding Cooperativity in a Three-stranded β-Sheet Model. Journal of Molecular Biology. 352(2). 370–381. 34 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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