Sergey Ovchinnikov

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 46

Top Venues

Nature

bioRxiv : the preprint server for biology

Nature structural & molecular biology

Proceedings of the National Academy of Sciences of the United States of America

University of Washington (PHD)

This page only lists publications with an associated author ORCID identifier.

Education History

University of Washington

United States

PHD :: Molecular and Cellular Biology / Biochemistry

Portland State University

United States

BSC :: Micro/Molecular Biology

Publications

Casper A Goverde, Martin Pacesa, Nicolas Goldbach, Lars J Dornfeld, Petra E M Balbi, Sandrine Georgeon, Stéphane Rosset, Srajan Kapoor, Jagrity Choudhury, Justas Dauparas, Christian Schellhaas, Simon Kozlov, Julien S Baker, Sergey Ovchinnikov, Alex J Vecchio, Bruno E Correia
Computational design of soluble and functional membrane protein analogues. Nature (2024)
Casper A Goverde, Martin Pacesa, Nicolas Goldbach, Lars J Dornfeld, Petra E M Balbi, Sandrine Georgeon, Stéphane Rosset, Srajan Kapoor, Jagrity Choudhury, Justas Dauparas, Christian Schellhaas, Simon Kozlov, Julien S Baker, Sergey Ovchinnikov, Alex J Vecchio, Bruno E Correia
Computational design of soluble and functional membrane protein analogues. Nature 631 (8020) (2024)
Casper A Goverde, Martin Pacesa, Nicolas Goldbach, Lars J Dornfeld, Petra E M Balbi, Sandrine Georgeon, Stéphane Rosset, Srajan Kapoor, Jagrity Choudhury, Justas Dauparas, Christian Schellhaas, Simon Kozlov, Julien S Baker, Sergey Ovchinnikov, Alex J Vecchio, Bruno E Correia
Computational design of soluble and functional membrane protein analogues. Nature 631 (8020) (2024)
Casper A Goverde, Martin Pacesa, Nicolas Goldbach, Lars J Dornfeld, Petra E M Balbi, Sandrine Georgeon, Stéphane Rosset, Srajan Kapoor, Jagrity Choudhury, Justas Dauparas, Christian Schellhaas, Simon Kozlov, David Baker, Sergey Ovchinnikov, Alex J Vecchio, Bruno E Correia
Computational design of soluble functional analogues of integral membrane proteins. bioRxiv : the preprint server for biology (2024)
Casper A Goverde, Martin Pacesa, Nicolas Goldbach, Lars J Dornfeld, Petra E M Balbi, Sandrine Georgeon, Stéphane Rosset, Srajan Kapoor, Jagrity Choudhury, Justas Dauparas, Christian Schellhaas, Simon Kozlov, Julien S Baker, Sergey Ovchinnikov, Alex J Vecchio, Bruno E Correia
Computational design of soluble and functional membrane protein analogues. Nature 631 (8020) (2024)
Casper A Goverde, Martin Pacesa, Nicolas Goldbach, Lars J Dornfeld, Petra E M Balbi, Sandrine Georgeon, Stéphane Rosset, Srajan Kapoor, Jagrity Choudhury, Justas Dauparas, Christian Schellhaas, Simon Kozlov, Julien S Baker, Sergey Ovchinnikov, Alex J Vecchio, Bruno E Correia
Computational design of soluble and functional membrane protein analogues. Nature 631 (8020) (2024)
Yunha Hwang, Andre L Cornman, Elizabeth H Kellogg, Sergey Ovchinnikov, Peter R Girguis
Genomic language model predicts protein co-regulation and function. Nature communications 15 (1) (2024)
Casper A Goverde, Martin Pacesa, Nicolas Goldbach, Lars J Dornfeld, Petra E M Balbi, Sandrine Georgeon, Stéphane Rosset, Srajan Kapoor, Jagrity Choudhury, Justas Dauparas, Christian Schellhaas, Simon Kozlov, David Baker, Sergey Ovchinnikov, Alex J Vecchio, Bruno E Correia
Computational design of soluble functional analogues of integral membrane proteins. bioRxiv : the preprint server for biology (2024)
Yunha Hwang, Andre L Cornman, Elizabeth H Kellogg, Sergey Ovchinnikov, Peter R Girguis
Genomic language model predicts protein co-regulation and function. Nature communications 15 (1) (2024)
Casper A Goverde, Martin Pacesa, Nicolas Goldbach, Lars J Dornfeld, Petra E M Balbi, Sandrine Georgeon, Stéphane Rosset, Srajan Kapoor, Jagrity Choudhury, Justas Dauparas, Christian Schellhaas, Simon Kozlov, Julien S Baker, Sergey Ovchinnikov, Alex J Vecchio, Bruno E Correia
Computational design of soluble and functional membrane protein analogues. Nature 631 (8020) (2024)
Yunha Hwang, Andre L Cornman, Elizabeth H Kellogg, Sergey Ovchinnikov, Peter R Girguis
Genomic language model predicts protein co-regulation and function. Nature communications 15 (1) (2024)
Casper A Goverde, Martin Pacesa, Nicolas Goldbach, Lars J Dornfeld, Petra E M Balbi, Sandrine Georgeon, Stéphane Rosset, Srajan Kapoor, Jagrity Choudhury, Justas Dauparas, Christian Schellhaas, Simon Kozlov, Julien S Baker, Sergey Ovchinnikov, Alex J Vecchio, Bruno E Correia
Computational design of soluble and functional membrane protein analogues. Nature 631 (8020) (2024)
Casper A Goverde, Martin Pacesa, Nicolas Goldbach, Lars J Dornfeld, Petra E M Balbi, Sandrine Georgeon, Stéphane Rosset, Srajan Kapoor, Jagrity Choudhury, Justas Dauparas, Christian Schellhaas, Simon Kozlov, Julien S Baker, Sergey Ovchinnikov, Alex J Vecchio, Bruno E Correia
Computational design of soluble and functional membrane protein analogues. Nature (2024)
Casper A Goverde, Martin Pacesa, Nicolas Goldbach, Lars J Dornfeld, Petra E M Balbi, Sandrine Georgeon, Stéphane Rosset, Srajan Kapoor, Jagrity Choudhury, Justas Dauparas, Christian Schellhaas, Simon Kozlov, Julien S Baker, Sergey Ovchinnikov, Alex J Vecchio, Bruno E Correia
Computational design of soluble and functional membrane protein analogues. Nature 631 (8020) (2024)
Casper A Goverde, Martin Pacesa, Nicolas Goldbach, Lars J Dornfeld, Petra E M Balbi, Sandrine Georgeon, Stéphane Rosset, Srajan Kapoor, Jagrity Choudhury, Justas Dauparas, Christian Schellhaas, Simon Kozlov, Julien S Baker, Sergey Ovchinnikov, Alex J Vecchio, Bruno E Correia
Computational design of soluble and functional membrane protein analogues. Nature (2024)
Casper A Goverde, Martin Pacesa, Nicolas Goldbach, Lars J Dornfeld, Petra E M Balbi, Sandrine Georgeon, Stéphane Rosset, Srajan Kapoor, Jagrity Choudhury, Justas Dauparas, Christian Schellhaas, Simon Kozlov, Julien S Baker, Sergey Ovchinnikov, Alex J Vecchio, Bruno E Correia
Computational design of soluble and functional membrane protein analogues. Nature (2024)
Casper A Goverde, Martin Pacesa, Nicolas Goldbach, Lars J Dornfeld, Petra E M Balbi, Sandrine Georgeon, Stéphane Rosset, Srajan Kapoor, Jagrity Choudhury, Justas Dauparas, Christian Schellhaas, Simon Kozlov, David Baker, Sergey Ovchinnikov, Alex J Vecchio, Bruno E Correia
Computational design of soluble functional analogues of integral membrane proteins. bioRxiv : the preprint server for biology (2024)
Casper A Goverde, Martin Pacesa, Nicolas Goldbach, Lars J Dornfeld, Petra E M Balbi, Sandrine Georgeon, Stéphane Rosset, Srajan Kapoor, Jagrity Choudhury, Justas Dauparas, Christian Schellhaas, Simon Kozlov, Julien S Baker, Sergey Ovchinnikov, Alex J Vecchio, Bruno E Correia
Computational design of soluble and functional membrane protein analogues. Nature 631 (8020) (2024)
Casper A Goverde, Martin Pacesa, Nicolas Goldbach, Lars J Dornfeld, Petra E M Balbi, Sandrine Georgeon, Stéphane Rosset, Srajan Kapoor, Jagrity Choudhury, Justas Dauparas, Christian Schellhaas, Simon Kozlov, David Baker, Sergey Ovchinnikov, Alex J Vecchio, Bruno E Correia
Computational design of soluble functional analogues of integral membrane proteins. bioRxiv : the preprint server for biology (2024)
Stephen A Rettie, Katelyn V Campbell, Asim K Bera, Alex Kang, Simon Kozlov, Joshmyn De La Cruz, Victor Adebomi, Guangfeng Zhou, Frank Dimaio, Sergey Ovchinnikov, Gaurav Bhardwaj
Cyclic peptide structure prediction and design using AlphaFold. bioRxiv : the preprint server for biology (2023)
David Edwin 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, Julien S Baker
De novo design of small beta barrel proteins. Proceedings of the National Academy of Sciences of the United States of America 120 (11) (2023)
Joseph L Watson, David Juergens, Nathaniel R Bennett, Brian L Trippe, Jason Yim, Helen E Eisenach, Woody Ahern, Andrew J Borst, Robert J Ragotte, Lukas F Milles, Basile I M Wicky, Nikita Hanikel, Samuel J Pellock, Alexis Courbet, William Sheffler, Jue Wang, Preetham Venkatesh, Isaac Sappington, Susana Vázquez Torres, Anna Lauko, Valentin De Bortoli, Emile Mathieu, Sergey Ovchinnikov, Regina Barzilay, Tommi S Jaakkola, Frank DiMaio, Minkyung Baek, Julien S Baker
De novo design of protein structure and function with RFdiffusion. Nature (2023)
Quinton M Dowling, Hannah E Volkman, Elizabeth E Gray, Sergey Ovchinnikov, Stephanie Cambier, Asim K Bera, Banumathi Sankaran, Max R Johnson, Matthew J Bick, Alex Kang, Daniel B Stetson, Neil P King
Computational design of constitutively active cGAS. Nature structural & molecular biology (2023)
Quinton M Dowling, Hannah E Volkman, Elizabeth E Gray, Sergey Ovchinnikov, Stephanie Cambier, Asim K Bera, Banumathi Sankaran, Max R Johnson, Matthew J Bick, Alex Kang, Daniel B Stetson, Neil P King
Computational design of constitutively active cGAS. Nature structural & molecular biology 30 (1) (2023)
Georgios A Pavlopoulos, Fotis A Baltoumas, Sirui Liu, Oguz Selvitopi, Antonio Pedro Camargo, Stephen Nayfach, Ariful Azad, Simon Roux, Lee Call, Natalia N Ivanova, I Min Chen, A David Páez-Espino, Evangelos Karatzas, null null, Ioannis Iliopoulos, Konstantinos T Konstantinidis, James M Tiedje, Jennifer Pett-Ridge, Julien S Baker, Axel Visel, Christos A Ouzounis, Sergey Ovchinnikov, Aydın Buluç, Nikos C Kyrpides
Unraveling the functional dark matter through global metagenomics. Nature (2023)
David Edwin 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, Julien S Baker
De novo design of small beta barrel proteins. Proceedings of the National Academy of Sciences of the United States of America 120 (11) (2023)
David Edwin 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, Julien S Baker
De novo design of small beta barrel proteins. Proceedings of the National Academy of Sciences of the United States of America 120 (11) (2023)
Stephen A Rettie, Katelyn V Campbell, Asim K Bera, Alex Kang, Simon Kozlov, Joshmyn De La Cruz, Victor Adebomi, Guangfeng Zhou, Frank Dimaio, Sergey Ovchinnikov, Gaurav Bhardwaj
Cyclic peptide structure prediction and design using AlphaFold. bioRxiv : the preprint server for biology (2023)
Hannah K Wayment-Steele, Adedolapo M Ojoawo, Renee Otten, Julia M Apitz, Warintra Pitsawong, Marc Hömberger, Sergey Ovchinnikov, Lucy J Colwell, Dorothee Kern
Predicting multiple conformations via sequence clustering and AlphaFold2. Nature (2023)
Yao Cheng, Haobo Wang, Hua Xu, Yuan Liu, Bin Ma, Xuemin Chen, Xin Zeng, Xianghe Wang, Bo Wang, Carina Shiau, Sergey Ovchinnikov, Xiao-Dong Su, Chu Wang
Co-evolution-based prediction of metal-binding sites in proteomes by machine learning. Nature chemical biology (2023)
Quinton M Dowling, Hannah E Volkman, Elizabeth E Gray, Sergey Ovchinnikov, Stephanie Cambier, Asim K Bera, Banumathi Sankaran, Max R Johnson, Matthew J Bick, Alex Kang, Daniel B Stetson, Neil P King
Computational design of constitutively active cGAS. Nature structural & molecular biology 30 (1) (2023)
Quinton M Dowling, Hannah E Volkman, Elizabeth E Gray, Sergey Ovchinnikov, Stephanie Cambier, Asim K Bera, Banumathi Sankaran, Max R Johnson, Matthew J Bick, Alex Kang, Daniel B Stetson, Neil P King
Computational design of constitutively active cGAS. Nature structural & molecular biology 30 (1) (2023)
Kotaro Tsuboyama, Justas Dauparas, Jonathan Chen, Elodie Laine, Yasser Mohseni Behbahani, Jonathan J Weinstein, Niall M Mangan, Sergey Ovchinnikov, Gabriel J Rocklin
Mega-scale experimental analysis of protein folding stability in biology and design. Nature (2023)
Quinton M Dowling, Hannah E Volkman, Elizabeth E Gray, Sergey Ovchinnikov, Stephanie Cambier, Asim K Bera, Banumathi Sankaran, Max R Johnson, Matthew J Bick, Alex Kang, Daniel B Stetson, Neil P King
Computational design of constitutively active cGAS. Nature structural & molecular biology 30 (1) (2023)
Stephen A Rettie, Katelyn V Campbell, Asim K Bera, Alex Kang, Simon Kozlov, Joshmyn De La Cruz, Victor Adebomi, Guangfeng Zhou, Frank Dimaio, Sergey Ovchinnikov, Gaurav Bhardwaj
Cyclic peptide structure prediction and design using AlphaFold. bioRxiv : the preprint server for biology (2023)
Milot Mirdita, Konstantin Schütze, Yoshitaka Moriwaki, Lim Heo, Sergey Ovchinnikov, Martin Steinegger
ColabFold: making protein folding accessible to all. Nature methods 19 (6) (2022)
Mehmet Akdel, Douglas E V Pires, Eduard Porta Pardo, Jürgen Jänes, Arthur O Zalevsky, Bálint Mészáros, Patrick Bryant, Lydia L Good, Roman A Laskowski, Gabriele Pozzati, Aditi Shenoy, Wensi Zhu, Petras Kundrotas, Victoria Ruiz Serra, Carlos Henrique Miranda, Alistair S Dunham, David Francis Burke, Neera Borkakoti, Sameer Velankar, Adam Frost, Jérôme Basquin, Kresten Lindorff-Larsen, Alex Bateman, Andrey V Kajava, Alfonso Valencia, Sergey Ovchinnikov, Janani Durairaj, David Benjamin Ascher, Janet M Thornton, Norman E Davey, Amelie Stein, Arne Elofsson, Tristan I Croll, Pedro Beltrao
A structural biology community assessment of AlphaFold2 applications. Nature structural & molecular biology 29 (11) (2022)
Jue Wang, Sidney Lisanza, David C Juergens, Doug K Tischer, Joseph L Watson, Karla M Castro, Robert J Ragotte, Amijai Saragovi, Lukas F Milles, Minkyung Baek, David Baker, Wei Yang, Derrick R Hicks, Marc Expòsit, Thomas Schlichthaerle, Jung-Ho Chun, Justas Dauparas, Nathaniel R Bennett, Basile I M Wicky, Andrew Muenks, Frank Dimaio, Bruno E Correia, Sergey Ovchinnikov, Julien S Baker
Scaffolding protein functional sites using deep learning. Science (New York, N.Y.) 377 (6604) (2022)
David Baker, Samuel J Pellock, Tamuka M Chidyausiku, Theresa A Ramelot, Sergey Ovchinnikov, Jingzhou Hao, Khushboo Bafna, Christoffer H Norn, Alex Kang, Asim K Bera, Frank DiMaio, Lauren Carter, Cameron M Chow, Gaetano T Montelione, Julien S Baker
De novo protein design by deep network hallucination. Nature (2021)
Minkyung Baek, Frank Dimaio, David Baker, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Nick V Grishin, Lisa N Kinch, R Dustin Schaeffer, Claudia Millán, Hahnbeom Park, Carson Adams, Caleb R Glassman, Andy DeGiovanni, Jose Henrique Pereira, Andria V Rodrigues, Alberdina A van Dijk, Ana C Ebrecht, Diederik Johannes Opperman, Theo Sagmeister, Christoph Buhlheller, Tea Pavkov-Keller, Manoj K Rathinaswamy, Udit Dalwadi, Calvin K Yip, John E Burke, K Christopher Garcia, Nick V Grishin, Paul D Adams, Randy J Read, Julien S Baker
Accurate prediction of protein structures and interactions using a three-track neural network. Science (New York, N.Y.) 373 (6557) (2021)
Ian R Humphreys, Jimin Pei, Minkyung Baek, Aditya Krishnakumar, David Baker, Sergey Ovchinnikov, Jing Zhang, Travis J Ness, Sudeep Banjade, Saket Rahul Bagde, Viktoriya G Stancheva, Xiao-Han Li, Kaixian Liu, Zhi Zheng, Daniel J Barrero, Upasana Roy, Jochen Kuper, Israel S Fernández, Barnabas Szakal, Dana Branzei, Josep Rizo, Caroline Kisker, Eric C Greene, Sue Biggins, Scott Keeney, Elizabeth A Miller, J Christopher Fromme, Tamara L Hendrickson, Nick V Grishin, Julien S Baker
Computed structures of core eukaryotic protein complexes. Science (New York, N.Y.) 374 (6573) (2021)
Christoffer H Norn, Basile I M Wicky, David Juergens, Sirui Liu, David Kim, Doug Tischer, Brian Koepnick, David Baker, null null, Julien S Baker, Sergey Ovchinnikov
Protein sequence design by conformational landscape optimization. Proceedings of the National Academy of Sciences of the United States of America 118 (11) (2021)
Connor J Cooper, Kaiyuan Zheng, Katherine W Rush, Alexander Johs, Brian C Sanders, Georgios A Pavlopoulos, Nikos C Kyrpides, Mircea Podar, Sergey Ovchinnikov, Stephen W Ragsdale, Jerry M Parks
Structure determination of the HgcAB complex using metagenome sequence data: insights into microbial mercury methylation. Communications biology 3 (1) (2020)
Xudong Wu, Marc Siggel, Sergey Ovchinnikov, Wei Mi, Vladimir Svetlov, Evgeny Nudler, Maofu Liao, Gerhard Hummer, Tom A Rapoport
Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex. Science (New York, N.Y.) 368 (6489) (2020)
Sergey Ovchinnikov, Hahnbeom Park, David E Kim, Frank Dimaio, David Baker
Protein structure prediction using Rosetta in CASP12. Proteins (2017)
Hahnbeom Park, David E Kim, Sergey Ovchinnikov, David Baker, Frank Dimaio
Automatic structure prediction of oligomeric assemblies using Robetta in CASP12. Proteins (2017)

Sergey Ovchinnikov.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Sergey Ovchinnikov