Tom Darden

68.1k total citations · 7 hit papers
49 papers, 55.7k citations indexed

About

Tom Darden is a scholar working on Molecular Biology, Materials Chemistry and Atomic and Molecular Physics, and Optics. According to data from OpenAlex, Tom Darden has authored 49 papers receiving a total of 55.7k indexed citations (citations by other indexed papers that have themselves been cited), including 30 papers in Molecular Biology, 10 papers in Materials Chemistry and 7 papers in Atomic and Molecular Physics, and Optics. Recurrent topics in Tom Darden's work include Protein Structure and Dynamics (13 papers), Enzyme Structure and Function (10 papers) and DNA and Nucleic Acid Chemistry (8 papers). Tom Darden is often cited by papers focused on Protein Structure and Dynamics (13 papers), Enzyme Structure and Function (10 papers) and DNA and Nucleic Acid Chemistry (8 papers). Tom Darden collaborates with scholars based in United States, France and Germany. Tom Darden's co-authors include Lee G. Pedersen, Darrin M. York, L. Perera, Hsing Lee, Max L. Berkowitz, Ulrich Essmann, Thomas E. Cheatham, Robert J. Woods, Alexey V. Onufriev and Carlos Simmerling and has published in prestigious journals such as Proceedings of the National Academy of Sciences, Journal of the American Chemical Society and Journal of Biological Chemistry.

In The Last Decade

Tom Darden

48 papers receiving 55.1k citations

Hit Papers

5 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.

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

1993 25.0k citations Tom Darden, Darrin M. York et al. The Journal of Chemical Physics profile →
A smooth particle mesh Ewald method

1995 18.3k citations Ulrich Essmann, L. Perera et al. The Journal of Chemical Physics profile →
The Amber biomolecular simulation programs

2005 7.5k citations David A. Case, Thomas E. Cheatham et al. Journal of Computational Chemistry profile →
Making optimal use of empirical energy functions: Force‐field parameterization in crystal space

2004 748 citations Tom Darden et al. profile →
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, Jennifer L. Miller et al. Journal of the American Chemical Society profile →
The effect of long-range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods

1993 609 citations Darrin M. York, Tom Darden et al. The Journal of Chemical Physics profile →
New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations

1999 556 citations Tom Darden, L. Perera et al. Structure profile →

Peers — A (Enhanced Table)

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

Name	h						Papers	Cites
Tom Darden United States	28	33.8k	9.7k	8.1k	5.8k	5.5k	49	55.7k
Lee G. Pedersen United States	43	29.2k 0.9×	8.7k 0.9×	7.8k 1.0×	5.7k 1.0×	5.2k 0.9×	222	50.5k
Jeffry D. Madura United States	37	24.2k 0.7×	8.3k 0.9×	9.7k 1.2×	4.6k 0.8×	5.5k 1.0×	127	43.4k
William Humphrey United States	21	24.5k 0.7×	12.8k 1.3×	5.2k 0.6×	7.5k 1.3×	5.9k 1.1×	39	53.5k
Barry Honig United States	108	37.5k 1.1×	9.0k 0.9×	6.9k 0.9×	3.9k 0.7×	2.9k 0.5×	347	51.3k
Alan E. Mark Australia	74	26.8k 0.8×	8.1k 0.8×	7.6k 0.9×	5.6k 1.0×	4.7k 0.8×	242	44.1k
Jeremy C. Smith United States	92	32.0k 0.9×	7.8k 0.8×	5.7k 0.7×	3.9k 0.7×	5.5k 1.0×	848	58.8k
Alexander D. MacKerell United States	93	38.9k 1.2×	9.1k 0.9×	10.7k 1.3×	6.0k 1.0×	4.9k 0.9×	473	57.6k
Andrew Dalke United States	9	26.7k 0.8×	13.0k 1.3×	5.1k 0.6×	7.5k 1.3×	5.9k 1.1×	13	56.0k
David van der Spoel Sweden	57	31.8k 0.9×	12.3k 1.3×	10.4k 1.3×	6.9k 1.2×	7.3k 1.3×	168	61.7k
Erik Lindahl Sweden	54	40.9k 1.2×	12.0k 1.2×	9.1k 1.1×	7.4k 1.3×	7.5k 1.4×	197	71.6k

Countries citing papers authored by Tom Darden

Since Specialization

Citations

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

Fields of papers citing papers by Tom Darden

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Tom Darden. 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 Tom Darden. The network helps show where Tom Darden may publish in the future.

Co-authorship network of co-authors of Tom Darden

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

All Works

Sort: Min cites: Since: Top N: Style:

20 of 20 papers shown

Elking, Dennis M., Tom Darden, & Robert J. Woods. (2007). Gaussian induced dipole polarization model. Journal of Computational Chemistry. 28(7). 1261–1274. 99 indexed citations

Case, David A., Thomas E. Cheatham, Tom Darden, et al.. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry. 26(16). 1668–1688. 7524 indexed citations breakdown →

Fisher, Timothy S., Tom Darden, & Vinayaka R. Prasad. (2003). Mutations Proximal to the Minor Groove-Binding Track of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Differentially Affect Utilization of RNA versus DNA as Template. Journal of Virology. 77(10). 5837–5845. 19 indexed citations

Negishi, Masahiko, Eric F. Johnson, Lars C. Pedersen, et al.. (2003). Explicit Water Near the Catalytic I Helix Thr in the Predicted Solution Structure of CYP2A4. Biophysical Journal. 84(1). 57–68. 15 indexed citations

Fisher, Timothy S., Tom Darden, & Vinayaka R. Prasad. (2002). Substitutions at Phe61 in the β3-β4 Hairpin of HIV-1 Reverse Transcriptase Reveal a Role for the Fingers Subdomain in Strand Displacement DNA Synthesis. Journal of Molecular Biology. 325(3). 443–459. 38 indexed citations

Inga, Alberto, Paola Monti, Gilberto Fronza, Tom Darden, & Michael A. Resnick. (2001). p53 mutants exhibiting enhanced transcriptional activation and altered promoter selectivity are revealed using a sensitive, yeast-based functional assay. Oncogene. 20(4). 501–513. 47 indexed citations

Caffrey, James J., Tom Darden, Markus R. Wenk, & Stephen B. Shears. (2001). Expanding coincident signaling by PTEN through its inositol 1,3,4,5,6‐pentakisphosphate 3‐phosphatase activity. FEBS Letters. 499(1-2). 6–10. 34 indexed citations

Darden, Tom, L. Perera, Leping Li, & Lee G. Pedersen. (1999). New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations. Structure. 7(3). R55–R60. 556 indexed citations breakdown →

Negishi, Masahiko, et al.. (1996). The roles of individual amino acids in altering substrate specificity of the P450 2a4/2a5 enzymes. Biochimie. 78(8-9). 685–694. 15 indexed citations

10.

Li, Leping, Tom Darden, Richard G. Hiskey, & Lee G. Pedersen. (1996). Computational Studies of Human Prothrombin Fragment 1 the Gla Domain of Factor IX and Several Biological Interesting Mutants. Pathophysiology of Haemostasis and Thrombosis. 26(Suppl. 1). 54–59. 2 indexed citations

11.

Li, Leping, Tom Darden, C. K. Foley, Richard G. Hiskey, & Lee G. Pedersen. (1995). Homology modeling and molecular dynamics simulation of human prothrombin fragment 1. Protein Science. 4(11). 2341–2348. 9 indexed citations

12.

Essmann, Ulrich, L. Perera, Max L. Berkowitz, et al.. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics. 103(19). 8577–8593. 18317 indexed citations breakdown →

13.

Cheatham, Thomas E., Jennifer L. Miller, Thomas Fox, Tom Darden, & Peter A. Kollman. (1995). 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. 117(14). 4193–4194. 717 indexed citations breakdown →

14.

York, Darrin M., Libero J. Bartolotti, Tom Darden, Lee G. Pedersen, & M W Anderson. (1994). Simulations of the solution structure of HIV‐1 protease in the presence and absence of bound zinc. Journal of Computational Chemistry. 15(1). 61–71. 5 indexed citations

15.

York, Darrin M., Alexander Wlodawer, Lee G. Pedersen, & Tom Darden. (1994). Atomic-level accuracy in simulations of large protein crystals.. Proceedings of the National Academy of Sciences. 91(18). 8715–8718. 147 indexed citations

16.

Frech, Matthias, Tom Darden, Lee G. Pedersen, et al.. (1994). Role of Glutamine-61 in the Hydrolysis of GTP by p21H-ras: An Experimental and Theoretical Study. Biochemistry. 33(11). 3237–3244. 112 indexed citations

17.

Darden, Tom, Darrin M. York, & Lee G. Pedersen. (1993). Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. The Journal of Chemical Physics. 98(12). 10089–10092. 25017 indexed citations breakdown →

18.

Darden, Tom & Lee G. Pedersen. (1993). Molecular modeling: an experimental tool.. Environmental Health Perspectives. 101(5). 410–412. 71 indexed citations

19.

Iwasaki, M., Tom Darden, Lee G. Pedersen, et al.. (1993). Engineering mouse P450coh to a novel corticosterone 15 alpha-hydroxylase and modeling steroid-binding orientation in the substrate pocket.. Journal of Biological Chemistry. 268(2). 759–762. 47 indexed citations

20.

Foley, C. K., Lee G. Pedersen, Paul S. Charifson, et al.. (1992). Simulation of the solution structure of the H-ras p21-GTP complex. Biochemistry. 31(21). 4951–4959. 38 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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