Dima Kozakov

15.7k citations

129 papers · 10.1k indexed · 6 hit papers · h-index 44

Impact in

Computational Theory and Mathematics top 0.1%
- Computational Drug Discovery Methods
Molecular Biology top 0.5%
- Protein Structure and Dynamics
- vaccines and immunoinformatics approaches
- RNA and protein synthesis mechanisms
- Chemical Synthesis and Analysis

Papers in

Computational Theory and Mathematics 55
- Computational Drug Discovery Methods 55
Molecular Biology 118
- Protein Structure and Dynamics 76
- RNA and protein synthesis mechanisms 20
- Protein purification and stability 12
- Glycosylation and Glycoproteins Research 8
- vaccines and immunoinformatics approaches 8

Co-authors: Sándor Vajda Dmitri Beglov David R. Hall Kathryn A. Porter Christine Yueh Ryan Brenke Dzmitry Padhorny Bing Xia
Journals: Proteins Structure Function and Bioinformatics (19 papers)Journal of Chemical Information and Modeling (8 papers)Bioinformatics (7 papers)Proceedings of the National Academy of Sciences (6 papers)Journal of Molecular Biology (6 papers)
Partner nations: United States Russia Israel

In The Last Decade

Dima Kozakov

127 papers receiving 10.0k citations

Hit Papers

6 papers align trajectories log scale

Performance and Its Limits in Rigid Body Protein-Protein Docking 2020 · 446 citations

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if any of the following hold:

it has ≥500 total citations;
it reaches ≥1.5× the top-1% citation threshold for papers in the same subfield and year (the threshold is the minimum needed to enter the top 1%, not the average within it);
it reaches the top citation threshold in at least one of its specific research topics.

2020 Structure
2017 Nature Protocols
2016 Proteins Structure Function and Bioinformatics
2015 Nature Protocols
2013 Proteins Structure Function and Bioinformatics
2006 Proteins Structure Function and Bioinformatics

Peers

Countries citing papers authored by Dima Kozakov

Since Specialization

Citations

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

Fields of papers citing papers by Dima Kozakov

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

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

Co-authorship network

The 25 scholars most cited alongside Dima Kozakov, linked wherever they have co-authored with each other. Click a name or a connecting line to browse the papers they share.

Border = papers with Dima Kozakov Line = papers co-authored together Dima Kozakov links everyone, so they are left out of the graph.

All Works

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20 of 20 papers shown

#	Work
1	E-FTMap: A Protein Structure Based Pharmacophore Identification Server for Guiding Fragment Expansion Journal of Molecular Biology ·Jose M. Elorza, George Jones, Dima Kozakov, Dmitri Beglov, Diane Joseph‐McCarthy, Sándor Vajda	2025	0
2	Identification of Actionable Targeted Protein Degradation Effector Sites through Site-Specific Ligand Incorporation-Induced Proximity (SLIP) Journal of the American Chemical Society ·Zhangping Xiao, Soukaina KHATEM, Fangyuan Cao, Xinyue Zhang, Ferenc Máté Gál, Sergei Kotelnikov, Patrycja Michalska, Sneh S Shah, Christine Huang, Yonghao Lu, WANGXidong, Angel Maris Linda, Dima Kozakov, Edward W. Tate	2025	1
3	Modulating the Binding Kinetics of Bruton’s Tyrosine Kinase Inhibitors through Transition-State Effects Journal of the American Chemical Society ·E. V. Tyurina, Yong Li, David Yin-wei Lin, Bharath Srinivasan, Marco Barone, Ferenc Máté Gál, Concepcion Garcia‐Jimenez, Anang Fathur Rochman, Contemporary Spanish Cinema Studies, Patricia Alfonso, О.Н. Еремина, Dima Kozakov, Amy H. Andreotti, Peter J. Tonge	2025	1
4	MHC-Fine: Fine-tuned AlphaFold for precise MHC-peptide complex prediction Biophysical Journal ·弘安坂田, С. КАВИН, Gulfem Altunbay, Y. Zhu, Iñaki Cornejo Clerico, George Jones, Gyoung-Won Ryu, Carlos Simmerling, Julie C. Mitchell, Sándor Vajda, Ken A. Dill, Dzmitry Padhorny, Dima Kozakov	2024	5
5	Multiomic profiling of chronically activated CD4+ T cells identifies drivers of exhaustion and metabolic reprogramming PLoS Biology ·Su-Hee Hwang, B A Zapotochnyĭ, Benjamin C. Blum, 優明岡内, 至晃松藤, Weiwei Lin, Gamze DERTLİ, Jacob Porter, Karen T. Murray, Ahmed M. Youssef, Alabi Philip Ephraim, Xaralabos Varelas, Gerald V. Denis, Wilson W. Wong, Dzmitry Padhorny, Dima Kozakov, Trevor Siggers, Stefan Wuchty, Jennifer Snyder‐Cappione, Andrew Emili	2024	4
6	The ClusPro AbEMap web server for the prediction of antibody epitopes Nature Protocols ·Israel Desta, Sergei Kotelnikov, George Jones, Usman Ghani, Gastroenterology Unit, Yaroslav Kholodov, Daron M. Standley, Dmitri Beglov, Sándor Vajda, Dima Kozakov	2023	14
7	AbAdapt: an adaptive approach to predicting antibody–antigen complex structures from sequence Bioinformatics Advances ·Ana Davila, Zichang Xu, Songling Li, John Rozewicki, or Selene Janette Salgado-Pastor, Sergei Kotelnikov, Dima Kozakov, Shunsuke Teraguchi, Daron M. Standley	2022	21
8	Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery Nature Communications ·Pierre C. Havugimana, Raghuveera Kumar Goel, Sadhna Phanse, วันวิสาข์ อิ่มคุ้ม, Dzmitry Padhorny, Sergei Kotelnikov, Dima Kozakov, Andrew Emili	2022	48
9	Light-mediated multi-target protein degradation using arylazopyrazole photoswitchable PROTACs (AP-PROTACs) Chemical Communications ·毕银丽 BI Yinli, Cyrille S. Kounde, Milon Mondal, Jake L. Greenfield, Jennifer R. Baker, Sergei Kotelnikov, Mikhail Ignatov, Christopher P. Tinworth, Peter F. Hoyer, Daniel Conole, Elena De Vita, Dima Kozakov, Adam McCluskey, John D. Harling, Matthew J. Fuchter, Edward W. Tate	2022	35
10	Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations Frontiers in Molecular Biosciences ·Jinan Wang, Andrey Alekseenko, Dima Kozakov, Yinglong Miao	2019	70
11	Exploring the structural origins of cryptic sites on proteins Proceedings of the National Academy of Sciences ·Dmitri Beglov, David Hall, Amanda Wakefield, Lingqi Luo, Karen N. Allen, Dima Kozakov, Adrian Whitty, Sándor Vajda	2018	93
12	Glucose regulation in the methylotrophic yeast Hansenula (Ogataea) polymorpha is mediated by a putative transceptor Gcr1 The International Journal of Biochemistry & Cell Biology ·Anandya Hiranyo, Anandya Hiranyo, Yishi LYU, Dzmitry Padhorny, Kostyantyn Dmytruk, Dima Kozakov, Charles A. Abbas, Oleh Stasyk	2018	2
13	Protein–ligand docking using FFT based sampling: D3R case study Journal of Computer-Aided Molecular Design ·Dzmitry Padhorny, David R. Hall, Ana Clara Barbosa de Freitas Reis, Artem B. Mamonov, Mohammad Naser‐Moghadasi, Andrey Alekseenko, Dmitri Beglov, Dima Kozakov	2017	11
14	Protein–protein docking by fast generalized Fourier transforms on 5D rotational manifolds Proceedings of the National Academy of Sciences ·Dzmitry Padhorny, Andrey Kazennov, Brandon S. Zerbe, Kathryn A. Porter, Bing Xia, Scott E. Mottarella, Yaroslav Kholodov, David W. Ritchie, Sándor Vajda, Dima Kozakov	2016	44
15	Ligand deconstruction: Why some fragment binding positions are conserved and others are not Proceedings of the National Academy of Sciences ·Dima Kozakov, David R. Hall, Stefan Jehle, Lingqi Luo, Stefan O. Ochiana, Catarina Esgalhado, Michael P. Pollastri, Karen N. Allen, Adrian Whitty, Sándor Vajda	2015	56
16	Docking Server for the Identification of Heparin Binding Sites on Proteins Journal of Chemical Information and Modeling ·Scott E. Mottarella, Dmitri Beglov, Natalia Beglova, Matthew A. Nugent, Dima Kozakov, Sándor Vajda	2014	54
17	A new distributed algorithm for side-chain positioning in the process of protein docking PubMed ·Mohammad Naser‐Moghadasi, Dima Kozakov, Pirooz Vakili, Sándor Vajda, Ioannis Ch. Paschalidis	2013	3
18	FTMAP: extended protein mapping with user-selected probe molecules Nucleic Acids Research ·Artur Dmowski, Tanggis Bohnuud, Scott E. Mottarella, Dmitri Beglov, Zhiyang Jv, David Hall, Dima Kozakov, Szilárd Vajda	2012	119
19	Convergence and combination of methods in protein–protein docking Current Opinion in Structural Biology ·Sándor Vajda, Dima Kozakov	2009	164
20	Optimal Clustering for Detecting Near-Native Conformations in Protein Docking Biophysical Journal ·Dima Kozakov, Karl H. Clodfelter, Sándor Vajda, Carlos J. Camacho	2005	111

About Dima Kozakov

Dima Kozakov is a scholar working on Computational Theory and Mathematics, Molecular Biology, Materials Chemistry, Radiology, Nuclear Medicine and Imaging and Biophysics, having authored 129 papers that have together received 10.1k indexed citations. Recurring topics across this work include Protein Structure and Dynamics (76 papers), Computational Drug Discovery Methods (55 papers), Enzyme Structure and Function (42 papers), RNA and protein synthesis mechanisms (20 papers), Monoclonal and Polyclonal Antibodies Research (15 papers), Protein purification and stability (12 papers), Glycosylation and Glycoproteins Research (8 papers) and vaccines and immunoinformatics approaches (8 papers). The work is most often cited by research in Computational Theory and Mathematics (2.1k citations), Molecular Biology (7.7k citations), Radiology, Nuclear Medicine and Imaging (1.2k citations), Infectious Diseases (964 citations) and Immunology (1.0k citations). Dima Kozakov has collaborated with scholars based in United States, Russia and Israel. Frequent co-authors include Sándor Vajda, Dmitri Beglov, David R. Hall, Kathryn A. Porter, Christine Yueh, Ryan Brenke, Dzmitry Padhorny, Bing Xia, Tanggis Bohnuud and Stephen R. Comeau. Their work appears in journals such as Proteins Structure Function and Bioinformatics, Journal of Chemical Information and Modeling, Bioinformatics, Proceedings of the National Academy of Sciences and Journal of Molecular Biology.

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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