David E. Kim

11.8k total citations · 6 hit papers
58 papers, 6.6k citations indexed

About

David E. Kim is a scholar working on Molecular Biology, Materials Chemistry and Urology. According to data from OpenAlex, David E. Kim has authored 58 papers receiving a total of 6.6k indexed citations (citations by other indexed papers that have themselves been cited), including 43 papers in Molecular Biology, 30 papers in Materials Chemistry and 6 papers in Urology. Recurrent topics in David E. Kim's work include Protein Structure and Dynamics (34 papers), Enzyme Structure and Function (30 papers) and RNA and protein synthesis mechanisms (10 papers). David E. Kim is often cited by papers focused on Protein Structure and Dynamics (34 papers), Enzyme Structure and Function (30 papers) and RNA and protein synthesis mechanisms (10 papers). David E. Kim collaborates with scholars based in United States, Japan and Belgium. David E. Kim's co-authors include David Baker, Dylan Chivian, Frank DiMaio, Tanja Kortemme, Hahnbeom Park, James Thompson, Ray Yu‐Ruei Wang, Yifan Song, Philip Bradley and Sergey Ovchinnikov and has published in prestigious journals such as Science, Proceedings of the National Academy of Sciences and JAMA.

In The Last Decade

David E. Kim

57 papers receiving 6.6k 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.

Protein structure prediction and analysis using the Robetta server

2004 1.6k citations David E. Kim, Dylan Chivian et al. profile →
High-Resolution Comparative Modeling with RosettaCM

2013 813 citations Frank DiMaio, Ray Yu‐Ruei Wang et al. profile →
Computational Alanine Scanning of Protein-Protein Interfaces

2004 460 citations David E. Kim, David Baker et al. profile →
Structure prediction for CASP8 with all‐atom refinement using Rosetta

2009 380 citations Srivatsan Raman, Robert M. Vernon et al. Proteins Structure Function and Bioinformatics profile →
Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules

2016 352 citations Hahnbeom Park, Philip Bradley et al. profile →
Protein structure determination using metagenome sequence data

2017 350 citations Sergey Ovchinnikov, Hahnbeom Park et al. Science profile →

Peers

Countries citing papers authored by David E. Kim

Since Specialization

Citations

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

Fields of papers citing papers by David E. Kim

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by David E. Kim. 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 David E. Kim. The network helps show where David E. Kim may publish in the future.

Co-authorship network of co-authors of David E. Kim

This figure shows the co-authorship network connecting the top 25 collaborators of David E. Kim. A scholar is included among the top collaborators of David E. Kim 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 David E. Kim. David E. Kim 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

#	Work	Indexed citations
1	Parametrically guided design of beta barrels and transmembrane nanopores using deep learning 2025 ·Proceedings of the National Academy of Sciences ·David E. Kim, Joseph L. Watson, David Juergens, Sagardip Majumder, (unknown), Stacey Gerben, Alex Kang, Asim K. Bera, Xinting Li, David Baker	2
2	Wide‐ranging genetic variation in sensitivity to rapamycin in Drosophila melanogaster 2024 ·Aging Cell ·Benjamin R. Harrison, Mitchell Lee, (unknown), (unknown), K. N. Han, (unknown), (unknown), (unknown), David E. Kim, (unknown), Yuchen Pan, (unknown), (unknown), (unknown), Danijel Djukovic, Daniel Raftery, Daniel Promislow	1
3	De novo design of small beta barrel proteins 2023 ·Proceedings of the National Academy of Sciences ·David E. Kim, Davin R. Jensen, David Feldman, Doug Tischer, Ayesha Saleem, Cameron M. Chow, Xinting Li, Lauren Carter, Lukas F. Milles, Hannah Nguyen, Alex Kang, Asim K. Bera, Francis C. Peterson, Brian F. Volkman, Sergey Ovchinnikov, David Baker	21
4	Ketogenic diet acutely improves gas exchange and sleep apnoea in obesity hypoventilation syndrome: A non‐randomized crossover study 2023 ·Respirology ·(unknown), Chenjuan Gu, David E. Kim, Daisy Duan, Bobbie J. Henry-Barron, Luu V. Pham, Vsevolod Y. Polotsky, Jonathan C. Jun	3
5	Protein homology model refinement by large-scale energy optimization 2018 ·Proceedings of the National Academy of Sciences ·Hahnbeom Park, Sergey Ovchinnikov, David E. Kim, Frank DiMaio, David Baker	47
6	Protein structure determination using metagenome sequence data breakdown → 2017 ·Science ·Sergey Ovchinnikov, Hahnbeom Park, Neha Varghese, Po‐Ssu Huang, Georgios A. Pavlopoulos, David E. Kim, Hetunandan Kamisetty, Nikos C. Kyrpides, David Baker	350
7	Comprehensive computational design of ordered peptide macrocycles 2017 ·Science ·Parisa Hosseinzadeh, Gaurav Bhardwaj, Vikram Khipple Mulligan, Matthew D. Shortridge, Timothy W. Craven, Fátima Pardo‐Ávila, Stephen Rettie, David E. Kim, Daniel‐Adriano Silva, Yehia Ibrahim, Ian Webb, John Cort, Joshua Adkins, Gabriele Varani, David Baker	156
8	Structure prediction using sparse simulated NOE restraints with Rosetta in CASP 11 2016 ·Proteins Structure Function and Bioinformatics ·Sergey Ovchinnikov, Hahnbeom Park, David E. Kim, Yuan Liu, Ray Yu‐Ruei Wang, David Baker	15
9	Improved de novo structure prediction in CASP 11 by incorporating coevolution information into Rosetta 2015 ·Proteins Structure Function and Bioinformatics ·Sergey Ovchinnikov, David E. Kim, Ray Yu‐Ruei Wang, Yuan Liu, Frank DiMaio, David Baker	77
10	Feature Selection Methods for Improving Protein Structure Prediction with Rosetta 2007 ·Neural Information Processing Systems ·(unknown), David Baker, Michael I. Jordan, Philip Bradley, Rhiju Das, David E. Kim	7
11	Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home 2007 ·Proteins Structure Function and Bioinformatics ·Rhiju Das, Bin Qian, Srivatsan Raman, Robert M. Vernon, James Thompson, Philip Bradley, Sagar D. Khare, Michael D. Tyka, (unknown), Dylan Chivian, David E. Kim, William Sheffler, Lars Malmström, Andrew M. Wollacott, Chu Wang, Ingemar André, David Baker	145
12	Physically realistic homology models built with rosetta can be more accurate than their templates 2006 ·Proceedings of the National Academy of Sciences ·Kira M.S. Misura, Dylan Chivian, Carol A. Rohl, David E. Kim, David Baker	135
13	Structure of Lmaj006129AAA, a hypothetical protein fromLeishmania major 2006 ·Acta Crystallographica Section F Structural Biology and Crystallization Communications ·T.L. Arakaki, Isolde Le Trong, Eric M. Phizicky, (unknown), George T. DeTitta, Joseph R. Luft, Angela Lauricella, Lori Anderson, Oleksandr Kalyuzhniy, Elizabeth A. Worthey, Peter J. Myler, David E. Kim, David Baker, Wim G. J. Hol, E.A. Merritt	19
14	Prediction of CASP6 structures using automated robetta protocols 2005 ·Proteins Structure Function and Bioinformatics ·Dylan Chivian, David E. Kim, Lars Malmström, Jack Schonbrun, Carol A. Rohl, David Baker	116
15	Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM 2005 ·Proteins Structure Function and Bioinformatics ·David E. Kim, Dylan Chivian, Lars Malmström, David Baker	87
16	Free modeling with Rosetta in CASP6 2005 ·Proteins Structure Function and Bioinformatics ·Philip Bradley, Lars Malmström, Bin Qian, Jack Schonbrun, Dylan Chivian, David E. Kim, Jens Meiler, Kira M.S. Misura, David Baker	110
17	Crystal structure of Bacillus subtilis YckF: structural and functional evolution 2004 ·Journal of Structural Biology ·Ruslan Sanishvili, (unknown), David E. Kim, James D. Watson, F. Collart, A. Joachimiak	9
18	The Relationship Between Ethical Business Practices, Government Regulations, and Consumer Rights 2002 ·Business and Professional Ethics Journal ·Shahid N. Bhuian, Alhassan G. Abdul‐Muhmin, David E. Kim	6
19	Accurate computer-based design of a new backbone conformation in the second turn of protein L 2002 ·Journal of Molecular Biology ·Brian Kuhlman, (unknown), David E. Kim, Kam Y. J. Zhang, David Baker	64
20	The single helix in protein L is largely disrupted at the rate-limiting step in folding 1998 ·Journal of Molecular Biology ·David E. Kim, Yi Qian, (unknown), Jonathan M. Goldberg, David Baker	45

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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