Sergey Ovchinnikov

Also affiliated with Massachusetts Institute of Technology

Biochemistry, Genetics and Molecular BiologyMaterials Science

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 47 papers. Top paper: “One-shot design of functional protein binders with BindCraft”.

One-shot design of functional protein binders with BindCraft

Nature(2025)10.1038/s41586-025-09429-6

N/A

1.9DataRank · unranked

181 citations

Lennart Nickel, Christian Schellhaas, Joseph Schmidt, Ekaterina Pyatova, Lucas Kissling +24 more

Advances in Chromatin and Chromosome Research: Perspectives from Multiple Fields

Molecular Cell(2020)10.1016/j.molcel.2020.07.003

N/A

1.6DataRank · unranked

65 citations

Assaf Amitai, Jason D. Buenrostro, Aditi Chakrabarti, Lingluo Chu, Anders S. Hansen +12 more

ColabFold: making protein folding accessible to all

Nature Methods(2022)10.1038/s41592-022-01488-1

N/A

1.4DataRank · unranked

9421 citations

Konstantin Schütze, Yoshitaka Moriwaki, Lim Heo, Sergey Ovchinnikov, Martin Steinegger +1 more

Accurate prediction of protein structures and interactions using a three-track neural network

Science(2021)10.1126/science.abj8754

N/A

1.3DataRank · unranked

5820 citations

Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee +27 more

Improved protein structure prediction using predicted interresidue orientations

Proceedings of the National Academy of Sciences(2020)10.1073/pnas.1914677117

N/A

1.1DataRank · unranked

1572 citations

Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker +1 more

A structural biology community assessment of AlphaFold2 applications

Nature Structural & Molecular Biology(2022)10.1038/s41594-022-00849-w

N/A

0.990DataRank · unranked

735 citations

Douglas E. V. Pires, Eduard Porta‐Pardo, Jürgen Jänes, Arthur O. Zalevsky, Bálint Mészáros +29 more

De novo protein design by deep network hallucination

Nature(2021)10.1038/s41586-021-04184-w

N/A

0.964DataRank · unranked

617 citations

Samuel J. Pellock, Tamuka M. Chidyausiku, Theresa A. Ramelot, Sergey Ovchinnikov, Jingzhou Hao +10 more

Scaffolding protein functional sites using deep learning

Science(2022)10.1126/science.abn2100

N/A

0.926DataRank · unranked

478 citations

Sidney Lisanza, David Juergens, Doug Tischer, Joseph L. Watson, Karla M. Castro +19 more

Transformer protein language models are unsupervised structure learners

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.15.422761

N/A

0.883DataRank · unranked

359 citations

Joshua Meier, Tom Sercu, Sergey Ovchinnikov, Alexander Rives, Roshan Rao

Protein language models learn evolutionary statistics of interacting sequence motifs

Proceedings of the National Academy of Sciences(2024)10.1073/pnas.2406285121

N/A

0.712DataRank · unranked

114 citations

Hannah K. Wayment-Steele, Garyk Brixi, Haobo Wang, Dorothee Kern, Sergey Ovchinnikov +1 more

Accurate de novo design of high-affinity protein-binding macrocycles using deep learning

Nature Chemical Biology(2025)10.1038/s41589-025-01929-w

N/A

0.612DataRank · unranked

58 citations

David Juergens, Victor Adebomi, Yensi Flores Bueso, Qinqin Zhao, Alexandria N. Leveille +21 more

Design of proteins presenting discontinuous functional sites using deep learning

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.29.402743

N/A

0.553DataRank · unranked

39 citations

Sidney Lisanza, Jue Wang, Runze Dong, Ivan Anishchenko, Lukas F. Milles +3 more

Single Layers of Attention Suffice to Predict Protein Contacts

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.21.423882

N/A

0.538DataRank · unranked

35 citations

Neil Thomas, Roshan Rao, Justas Dauparas, Peter K. Koo, David Baker +3 more

Protein sequence design by explicit energy landscape optimization

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.23.218917

N/A

0.520DataRank · unranked

31 citations

Basile I. M. Wicky, David Juergens, Sirui Liu, David E. Kim, Brian Koepnick +5 more

Protein language models learn evolutionary statistics of interacting sequence motifs

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.01.30.577970

N/A

0.494DataRank · unranked

26 citations

Hannah K. Wayment-Steele, Garyk Brixi, Haobo Wang, Matteo Dal Peraro, Dorothee Kern +2 more

Computational design of soluble functional analogues of integral membrane proteins

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.09.540044

N/A

0.470DataRank · unranked

22 citations

Martin Pačesa, Nicolas Goldbach, L Dornfeld, Petra E. M. Balbi, Sandrine Georgeon +11 more

De novo design of a peptide modulator to reverse sodium channel dysfunction linked to cardiac arrhythmias and epilepsy

Cell(2025)10.1016/j.cell.2025.07.038

N/A

0.442DataRank · unranked

18 citations

Bence Hegyi, Erin R. Cullen, Timothy M. Cho, Aaron Rodriques, Lucile Fossier +14 more

The structure-fitness landscape of pairwise relations in generative sequence models

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.29.402875

N/A

0.330DataRank · unranked

8 citations

Haobo Wang, Michael A. Stiffler, Justas Dauparas, Peter K. Koo, Sergey Ovchinnikov +1 more

Does Sequence Clustering Confound AlphaFold2?

Journal of Molecular Biology(2025)10.1016/j.jmb.2025.169376

N/A

0.104DataRank · unranked

1 citations

Sergey Ovchinnikov, Lucy J. Colwell, Dorothee Kern, Hannah K. Wayment-Steele

Deep learning methods for designing proteins scaffolding functional sites

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.10.468128

N/A

0DataRank · unranked

36 citations

Sidney Lisanza, David Juergens, Doug Tischer, Ivan Anishchenko, Minkyung Baek +10 more

State-of-the-Art Estimation of Protein Model Accuracy Using AlphaFold

Physical Review Letters(2022)10.1103/physrevlett.129.238101

N/A

0DataRank · unranked

269 citations

Sergey Ovchinnikov, James P. Roney

End-to-end learning of multiple sequence alignments with differentiable Smith–Waterman

Bioinformatics(2022)10.1093/bioinformatics/btac724

N/A

0DataRank · unranked

44 citations

Nicholas Bhattacharya, Roshan Rao, Justas Dauparas, Neil Thomas, Juannan Zhou +4 more

Language models generalize beyond natural proteins

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.21.521521

N/A

0DataRank · unranked

202 citations

Ori Kabeli, Yilun Du, Basile I. M. Wicky, Lukas F. Milles, Justas Dauparas +5 more

State-of-the-art estimation of protein model accuracy using AlphaFold

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.11.484043

N/A

0DataRank · unranked

48 citations

Sergey Ovchinnikov, James P. Roney

Disentanglement of Entropy and Coevolution using Spectral Regularization

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.04.483009

N/A

0DataRank · unranked

2 citations

Shihao Feng, Sirui Liu, Sergey Ovchinnikov, Haobo Wang

De novo design of small beta barrel proteins

Proceedings of the National Academy of Sciences(2023)10.1073/pnas.2207974120

N/A

0DataRank · unranked

36 citations

Davin R. Jensen, David Feldman, Doug Tischer, Ayesha Saleem, Cameron M. Chow +11 more

Computational design of constitutively active cGAS

Nature Structural & Molecular Biology(2023)10.1038/s41594-022-00862-z

N/A

0DataRank · unranked

19 citations

Hannah E. Volkman, Elizabeth Gray, Sergey Ovchinnikov, Stephanie Cambier, Asim K. Bera +7 more

Cyclic peptide structure prediction and design using AlphaFold

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.02.25.529956

N/A

0DataRank · unranked

81 citations

Katelyn V. Campbell, Asim K. Bera, Alex Kang, Simon Kozlov, Joshmyn De La Cruz +6 more

A structural biology community assessment of AlphaFold 2 applications

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.26.461876

N/A

0DataRank · unranked

143 citations

Douglas E. V. Pires, Eduard Porta‐Pardo, Jürgen Jänes, Arthur O. Zalevsky, Bálint Mészáros +26 more

Easy and accurate protein structure prediction using ColabFold

Research Square(2023)10.21203/rs.3.pex-2490/v1

N/A

0DataRank · unranked

21 citations

Sewon Lee, Eli Levy Karin, Hyunbin Kim, Yoshitaka Moriwaki, Sergey Ovchinnikov +3 more

Validation of de novo designed water-soluble and transmembrane proteins by in silico folding and melting

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.06.543955

N/A

0DataRank · unranked

5 citations

Carolin Berner, Sergey Ovchinnikov, Anastassia A. Vorobieva, Alvaro Martin Hermosilla

Easy and accurate protein structure prediction using ColabFold

Nature Protocols(2024)10.1038/s41596-024-01060-5

N/A

0DataRank · unranked

138 citations

Sewon Lee, Eli Levy Karin, Hyunbin Kim, Yoshitaka Moriwaki, Sergey Ovchinnikov +3 more

Computational design of soluble and functional membrane protein analogues

Nature(2024)10.1038/s41586-024-07601-y

N/A

0DataRank · unranked

126 citations

Martin Pačesa, Nicolas Goldbach, L Dornfeld, Petra E. M. Balbi, Sandrine Georgeon +11 more

Structure-based protein design with deep learning

Current Opinion in Chemical Biology(2021)10.1016/j.cbpa.2021.08.004

N/A

0DataRank · unranked

100 citations

Po‐Ssu Huang, Sergey Ovchinnikov

Genomic language model predicts protein co-regulation and function

Nature Communications(2024)10.1038/s41467-024-46947-9

N/A

0DataRank · unranked

89 citations

Andre Cornman, Elizabeth H. Kellogg, Sergey Ovchinnikov, Peter R. Girguis, Yunha Hwang

Scalable protein design using optimization in a relaxed sequence space

Science(2024)10.1126/science.adq1741

N/A

0DataRank · unranked

79 citations

Ali Khoshouei, Lara Fuβ, Dominik Schiwietz, Dominik Putz, Lara Weber +7 more

Validation of de novo designed water‐soluble and transmembrane β‐barrels by in silico folding and melting

Protein Science(2024)10.1002/pro.5033

N/A

0DataRank · unranked

21 citations

Carolin Berner, Sergey Ovchinnikov, Anastassia A. Vorobieva, Alvaro Martin Hermosilla

Disentanglement of Evolutionary Constraints in Statistical Models of Proteins

PRX Life(2024)10.1103/prxlife.2.023005

N/A

0DataRank · unranked

2 citations

Shihao Feng, Kotaro Tsuboyama, Sirui Liu, Gabriel J. Rocklin, Sergey Ovchinnikov +1 more

Protein sequence design by conformational landscape optimization

Proceedings of the National Academy of Sciences(2021)10.1073/pnas.2017228118

N/A

0DataRank · unranked

153 citations

Basile I. M. Wicky, David Juergens, Sirui Liu, David E. Kim, Doug Tischer +95 more

Solution NMR structure of Se0862, a highly conserved cyanobacterial protein involved in biofilm formation

Protein Science(2020)10.1002/pro.3952

N/A

0DataRank · unranked

10 citations

Yong‐Gang Chang, Roger Tseng, Sergey Ovchinnikov, Rakefet Schwarz, Andy LiWang +1 more

Cyclic peptide structure prediction and design using AlphaFold2

Nature Communications(2025)10.1038/s41467-025-59940-7

N/A

0DataRank · unranked

65 citations

Katelyn V. Campbell, Asim K. Bera, Alex Kang, Simon Kozlov, Yensi Flores Bueso +12 more

Structure determination of the HgcAB complex using metagenome sequence data: insights into microbial mercury methylation

Communications Biology(2020)10.1038/s42003-020-1047-5

N/A

0DataRank · unranked

53 citations

Kaiyuan Zheng, Katherine W. Rush, Alexander Johs, Brian Sanders, Georgios A. Pavlopoulos +6 more

Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex

Science(2020)10.1126/science.aaz2449

N/A

0DataRank · unranked

246 citations

Marc Siggel, Sergey Ovchinnikov, Wei Mi, Vladimir Svetlov, Evgeny Nudler +4 more

Stable de novo protein design via joint conformational landscape and sequence optimization

Nature Communications(2025)10.1038/s41467-025-66526-w

N/A

0DataRank · unranked

3 citations

J Dauparas, Kotaro Tsuboyama, Gabriel J. Rocklin, Sergey Ovchinnikov, Yehlin Cho

SoftAlign: End-to-end protein structures alignment

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.09.653096

N/A

0DataRank · unranked

1 citations

Samantha Petti, Sukhwan Park, Kithmini Herath, Michel van Kempen, Shihao Feng +4 more

Structures of core eukaryotic protein complexes

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.30.462231

N/A

0DataRank · unranked

15 citations

Jimin Pei, Minkyung Baek, Aditya Krishnakumar, Ivan Anishchenko, Sergey Ovchinnikov +22 more

De novo Design of a Peptide Modulator to Reverse Sodium Channel Dysfunction Linked to Cardiac Arrhythmias and Epilepsy

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.04.25.649609

N/A

0DataRank · unranked

0 citations

Bence Hegyi, Erin R. Cullen, Timothy M. Cho, Aaron Rodriques, Lucile Fossier +14 more