Ryan Brenke

2.5k total citations · 1 hit paper
13 papers, 1.9k citations indexed

About

Ryan Brenke is a scholar working on Molecular Biology, Computational Theory and Mathematics and Materials Chemistry. According to data from OpenAlex, Ryan Brenke has authored 13 papers receiving a total of 1.9k indexed citations (citations by other indexed papers that have themselves been cited), including 13 papers in Molecular Biology, 4 papers in Computational Theory and Mathematics and 4 papers in Materials Chemistry. Recurrent topics in Ryan Brenke's work include Protein Structure and Dynamics (7 papers), Protein purification and stability (4 papers) and Computational Drug Discovery Methods (4 papers). Ryan Brenke is often cited by papers focused on Protein Structure and Dynamics (7 papers), Protein purification and stability (4 papers) and Computational Drug Discovery Methods (4 papers). Ryan Brenke collaborates with scholars based in United States, Canada and Israel. Ryan Brenke's co-authors include Dima Kozakov, Sándor Vajda, Stephen R. Comeau, Dmitri Beglov, Gwo‐Yu Chuang, David R. Hall, Melissa Landon, Carla Mattos, Yang Shen and Tanggis Bohnuud and has published in prestigious journals such as Proceedings of the National Academy of Sciences, Nucleic Acids Research and Bioinformatics.

In The Last Decade

Ryan Brenke

13 papers receiving 1.9k 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.

PIPER: An FFT‐based protein docking program with pairwise potentials

2006 630 citations Dima Kozakov, Ryan Brenke et al. Proteins Structure Function and Bioinformatics profile →

Peers — A (Enhanced Table)

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

Name	h						Papers	Cites
Ryan Brenke United States	11	1.5k	536	333	266	183	13	1.9k
Howook Hwang United States	13	2.1k 1.4×	622 1.2×	533 1.6×	262 1.0×	209 1.1×	18	2.5k
Andrew A. Bogan United States	6	1.9k 1.3×	379 0.7×	432 1.3×	328 1.2×	157 0.9×	8	2.3k
Stephen R. Comeau United States	11	2.1k 1.3×	441 0.8×	433 1.3×	371 1.4×	317 1.7×	19	2.7k
Tanggis Bohnuud United States	11	1.5k 1.0×	373 0.7×	173 0.5×	343 1.3×	271 1.5×	14	2.0k
Scott E. Mottarella United States	7	1.2k 0.8×	310 0.6×	154 0.5×	203 0.8×	207 1.1×	9	1.7k
Brian Jiménez‐García Spain	19	1.6k 1.0×	389 0.7×	302 0.9×	290 1.1×	157 0.9×	30	1.9k
Sergey Lyskov United States	14	1.6k 1.1×	226 0.4×	323 1.0×	435 1.6×	215 1.2×	19	2.1k
David Gatchell United States	9	1.3k 0.8×	267 0.5×	315 0.9×	168 0.6×	171 0.9×	27	1.7k
Anna Vangone Netherlands	19	1.9k 1.2×	526 1.0×	342 1.0×	353 1.3×	279 1.5×	30	2.6k
Irene Luque Spain	27	1.4k 0.9×	302 0.6×	406 1.2×	139 0.5×	107 0.6×	65	2.2k

Countries citing papers authored by Ryan Brenke

Since Specialization

Citations

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

Fields of papers citing papers by Ryan Brenke

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

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

Co-authorship network of co-authors of Ryan Brenke

This figure shows the co-authorship network connecting the top 25 collaborators of Ryan Brenke. A scholar is included among the top collaborators of Ryan Brenke 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 Ryan Brenke. Ryan Brenke 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:

13 of 13 papers shown

Bohnuud, Tanggis, Dmitri Beglov, Brandon S. Zerbe, et al.. (2012). Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde. Nucleic Acids Research. 40(16). 7644–7652. 33 indexed citations

Brenke, Ryan, David R. Hall, Gwo‐Yu Chuang, et al.. (2012). Application of asymmetric statistical potentials to antibody–protein docking. Bioinformatics. 28(20). 2608–2614. 153 indexed citations

Beglov, Dmitri, David R. Hall, Ryan Brenke, et al.. (2011). Minimal ensembles of side chain conformers for modeling protein–protein interactions. Proteins Structure Function and Bioinformatics. 80(2). 591–601. 23 indexed citations

Kozakov, Dima, David R. Hall, Gwo‐Yu Chuang, et al.. (2011). Structural conservation of druggable hot spots in protein–protein interfaces. Proceedings of the National Academy of Sciences. 108(33). 13528–13533. 186 indexed citations

Kozakov, Dima, David R. Hall, Dmitri Beglov, et al.. (2010). Achieving reliability and high accuracy in automated protein docking: Cluspro, PIPER, SDU, and stability analysis in CAPRI rounds 13–19. Proteins Structure Function and Bioinformatics. 78(15). 3124–3130. 201 indexed citations

Brenke, Ryan, Dima Kozakov, Gwo‐Yu Chuang, et al.. (2009). Fragment-based identification of druggable ‘hot spots’ of proteins using Fourier domain correlation techniques. Bioinformatics. 25(5). 621–627. 364 indexed citations

Landon, Melissa, Raquel L. Lieberman, Quyen Q. Hoang, et al.. (2009). Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase. Journal of Computer-Aided Molecular Design. 23(8). 491–500. 71 indexed citations

Chuang, Gwo‐Yu, Dima Kozakov, Ryan Brenke, et al.. (2009). Binding Hot Spots and Amantadine Orientation in the Influenza A Virus M2 Proton Channel. Biophysical Journal. 97(10). 2846–2853. 35 indexed citations

Beglov, Dmitri, Changjin Lee, Alfredo De Biasio, et al.. (2009). Structural insights into recognition of β2‐glycoprotein I by the lipoprotein receptors. Proteins Structure Function and Bioinformatics. 77(4). 940–949. 9 indexed citations

10.

Chuang, Gwo‐Yu, Dima Kozakov, Ryan Brenke, Stephen R. Comeau, & Sándor Vajda. (2008). DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking. Biophysical Journal. 95(9). 4217–4227. 129 indexed citations

11.

Comeau, Stephen R., Dima Kozakov, Ryan Brenke, et al.. (2007). ClusPro: Performance in CAPRI rounds 6–11 and the new server. Proteins Structure Function and Bioinformatics. 69(4). 781–785. 69 indexed citations

12.

Shen, Yang, Ryan Brenke, Dima Kozakov, et al.. (2007). Docking with PIPER and refinement with SDU in rounds 6–11 of CAPRI. Proteins Structure Function and Bioinformatics. 69(4). 734–742. 10 indexed citations

13.

Kozakov, Dima, Ryan Brenke, Stephen R. Comeau, & Sándor Vajda. (2006). PIPER: An FFT‐based protein docking program with pairwise potentials. Proteins Structure Function and Bioinformatics. 65(2). 392–406. 630 indexed citations breakdown →

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.

Explore authors with similar magnitude of impact