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ArticlesPeer ReviewedFull Text
Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information
Author / Creator:Ovchinnikov, Sergey ; Kamisetty, Hetunandan ; Baker, David
Publisher:England: eLife Sciences Publications Ltd
Journal title:eLife, 2014-05, Vol.3, p.e02030-e02030
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Improved protein structure prediction using predicted interresidue orientations
Author / Creator:Yang, Jianyi ; Anishchenko, Ivan ; Park, Hahnbeom ; Peng, Zhenling ; Ovchinnikov, Sergey ; Baker, David
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2020-01, Vol.117 (3), p.1496-1503
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ArticlesPeer ReviewedFull Text
Assessing the utility of coevolution-based residue–residue contact predictions in a sequence- and structure-rich era
Author / Creator:Kamisetty, Hetunandan ; Ovchinnikov, Sergey ; Baker, David
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2013-09, Vol.110 (39), p.15674-15679
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ArticlesPeer ReviewedFull Text
Predicting multiple conformations via sequence clustering and AlphaFold2
Author / Creator:Wayment-Steele, Hannah K. ; Ojoawo, Adedolapo ; Otten, Renee ; Apitz, Julia M. ; Pitsawong, Warintra ; Hömberger, Marc ; Ovchinnikov, Sergey ; Colwell, Lucy ; Kern, Dorothee
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2024-01, Vol.625 (7996), p.832-839
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ArticlesPeer ReviewedFull Text
Protein structure determination using metagenome sequence data
Author / Creator:Ovchinnikov, Sergey ; Park, Hahnbeom ; Varghese, Neha ; Huang, Po-Ssu ; Pavlopoulos, Georgios A. ; Kim, David E. ; Kamisetty, Hetunandan ; Kyrpides, Nikos C. ; Baker, David
Publisher:United States: American Association for the Advancement of Science
Journal title:Science (American Association for the Advancement of Science), 2017-01, Vol.355 (6322), p.294-298
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A structural biology community assessment of AlphaFold2 applications
Author / Creator:Akdel, Mehmet ; Pires, Douglas E. V. ; Pardo, Eduard Porta ; Jänes, Jürgen ; Zalevsky, Arthur O. ; Mészáros, Bálint ; Bryant, Patrick ; Good, Lydia L. ; Laskowski, Roman A. ; Pozzati, Gabriele ; Shenoy, Aditi ; Zhu, Wensi ; Kundrotas, Petras ; Serra, Victoria Ruiz ; Rodrigues, Carlos H. M. ; Dunham, Alistair S. ; Burke, David ; Borkakoti, Neera ; Velankar, Sameer ; Frost, Adam ; Basquin, Jérôme ; Lindorff-Larsen, Kresten ; Bateman, Alex ; Kajava, Andrey V. ; Valencia, Alfonso ; Ovchinnikov, Sergey ; Durairaj, Janani ; Ascher, David B. ; Thornton, Janet M. ; Davey, Norman E. ; Stein, Amelie ; Elofsson, Arne ; Croll, Tristan I. ; Beltrao, Pedro
Publisher:New York: Nature Publishing Group US
Journal title:Nature structural & molecular biology, 2022-11, Vol.29 (11), p.1056-1067
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ArticlesPeer ReviewedFull Text
Protein homology model refinement by large-scale energy optimization
Author / Creator:Park, Hahnbeom ; Ovchinnikov, Sergey ; Kim, David E. ; DiMaio, Frank ; Baker, David
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2018-03, Vol.115 (12), p.3054-3059
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ArticlesPeer ReviewedFull Text
Genomic language model predicts protein co-regulation and function
Author / Creator:Hwang, Yunha ; Cornman, Andre L. ; Kellogg, Elizabeth H. ; Ovchinnikov, Sergey ; Girguis, Peter R.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2024-04, Vol.15 (1), p.2880-13, Article 2880
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ArticlesPeer ReviewedFull Text
Structure of a bd oxidase indicates similar mechanisms for membrane-integrated oxygen reductases
Author / Creator:Safarian, Schara ; Rajendran, Chitra ; Müller, Hannelore ; Preu, Julia ; Langer, Julian D. ; Ovchinnikov, Sergey ; Hirose, Taichiro ; Kusumoto, Tomoichirou ; Sakamoto, Junshi ; Michel, Hartmut
Publisher:United States: American Association for the Advancement of Science
Journal title:Science (American Association for the Advancement of Science), 2016-04, Vol.352 (6285), p.583-586
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ArticlesPeer ReviewedFull Text
Large-scale determination of previously unsolved protein structures using evolutionary information
Author / Creator:Ovchinnikov, Sergey ; Kinch, Lisa ; Park, Hahnbeom ; Liao, Yuxing ; Pei, Jimin ; Kim, David E ; Kamisetty, Hetunandan ; Grishin, Nick V ; Baker, David
Publisher:England: eLife Sciences Publications, Ltd
Journal title:eLife, 2015-09, Vol.4, p.e09248-e09248
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ArticlesPeer ReviewedFull Text
One- and Two-Particle Correlation Functions in the Cluster Perturbation Theory for Cuprates
Author / Creator:Kuz’min, Valerii I. ; Nikolaev, Sergey V. ; Korshunov, Maxim M. ; Ovchinnikov, Sergey G.
Publisher:Switzerland: MDPI AG
Journal title:Materials, 2023-06, Vol.16 (13), p.4640
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ArticlesPeer ReviewedFull Text
Magnetic Collapse in Fe3Se4 under High Pressure
Author / Creator:Begunovich, Lyudmila V. ; Korshunov, Maxim M. ; Ovchinnikov, Sergey G.
Publisher:Basel: MDPI AG
Journal title:Materials, 2022-06, Vol.15 (13), p.4583
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ArticlesPeer ReviewedFull Text
Quench dynamics and defects formation in the Ising chain in a transverse magnetic field
Author / Creator:Nesterov, Alexander I. ; Ramírez, Mónica F. ; Ovchinnikov, Sergey G.
Publisher:Berlin/Heidelberg: Springer Berlin Heidelberg
Journal title:The European physical journal. B, Condensed matter physics, 2022-04, Vol.95 (4), Article 73
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ArticlesPeer ReviewedFull Text
Cyclic peptide structure prediction and design using AlphaFold2
Author / Creator:Rettie, Stephen A. ; Campbell, Katelyn V. ; Bera, Asim K. ; Kang, Alex ; Kozlov, Simon ; Bueso, Yensi Flores ; De La Cruz, Joshmyn ; Ahlrichs, Maggie ; Cheng, Suna ; Gerben, Stacey R. ; Lamb, Mila ; Murray, Analisa ; Adebomi, Victor ; Zhou, Guangfeng ; DiMaio, Frank ; Ovchinnikov, Sergey ; Bhardwaj, Gaurav
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2025-05, Vol.16 (1), p.4730-15, Article 4730
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ArticlesPeer ReviewedFull Text
Computational design of constitutively active cGAS
Author / Creator:Dowling, Quinton M. ; Volkman, Hannah E. ; Gray, Elizabeth E. ; Ovchinnikov, Sergey ; Cambier, Stephanie ; Bera, Asim K. ; Sankaran, Banumathi ; Johnson, Max R. ; Bick, Matthew J. ; Kang, Alex ; Stetson, Daniel B. ; King, Neil P.
Publisher:New York: Nature Publishing Group US
Journal title:Nature structural & molecular biology, 2023-01, Vol.30 (1), p.72-80
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ArticlesPeer ReviewedFull Text
Pseudoscorpion mitochondria show rearranged genes and genome-wide reductions of RNA gene sizes and inferred structures, yet typical nucleotide composition bias
Author / Creator:Ovchinnikov, Sergey ; Masta, Susan E
Publisher:England: BioMed Central Ltd
Journal title:BMC evolutionary biology, 2012-03, Vol.12 (1), p.31-31
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Patterns and drivers of diatom diversity and abundance in the global ocean
Author / Creator:Pierella Karlusich, Juan J. ; Cosnier, Karen ; Zinger, Lucie ; Henry, Nicolas ; Nef, Charlotte ; Bernard, Guillaume ; Scalco, Eleonora ; Dvorak, Etienne ; Rocha Jimenez Vieira, Fabio ; Delage, Erwan ; Chaffron, Samuel ; Ovchinnikov, Sergey ; Zingone, Adriana ; Bowler, Chris
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2025-04, Vol.16 (1), p.3452-21, Article 3452
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Electronic Structure and Minimal Models for Flat and Corrugated CuO Monolayers: An Ab Initio Study
Author / Creator:Slobodchikov, Anatoly A. ; Nekrasov, Igor A. ; Begunovich, Lyudmila V. ; Makarov, Ilya A. ; Korshunov, Maxim M. ; Ovchinnikov, Sergey G.
Publisher:Switzerland: MDPI AG
Journal title:Materials, 2023-01, Vol.16 (2), p.658
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Effect of Multiplicity Fluctuation in Cobalt Ions on Crystal Structure, Magnetic and Electrical Properties of NdCoO3 and SmCoO3
Author / Creator:Dudnikov, Vyacheslav A. ; Orlov, Yuri S. ; Solovyov, Leonid A. ; Vereshchagin, Sergey N. ; Gavrilkin, Sergey Yu ; Tsvetkov, Alexey Yu ; Velikanov, Dmitriy A. ; Gorev, Michael V. ; Novikov, Sergey V. ; Ovchinnikov, Sergey G.
Publisher:Basel: MDPI AG
Journal title:Molecules (Basel, Switzerland), 2020-03, Vol.25 (6), p.1301
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Four steps for revealing and adjusting the 3D structure of aptamers in solution by small-angle X-ray scattering and computer simulation
Author / Creator:Tomilin, Felix N. ; Moryachkov, Roman ; Shchugoreva, Irina ; Zabluda, Vladimir N. ; Peters, Georgy ; Platunov, Mikhail ; Spiridonova, Vera ; Melnichuk, Anastasia ; Atrokhova, Anastasia ; Zamay, Sergey S. ; Ovchinnikov, Sergey G. ; Zamay, Galina S. ; Sokolov, Alexey ; Zamay, Tatiana N. ; Berezovski, Maxim V. ; Kichkailo, Anna S.
Publisher:Berlin/Heidelberg: Springer Berlin Heidelberg
Journal title:Analytical and bioanalytical chemistry, 2019-10, Vol.411 (25), p.6723-6732
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Showing 1 to 20 of 92 results

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Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

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Improved protein structure prediction using predicted interresidue orientations

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Assessing the utility of coevolution-based residue–residue contact predictions in a sequence- and structure-rich era

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Predicting multiple conformations via sequence clustering and AlphaFold2

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Protein structure determination using metagenome sequence data

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A structural biology community assessment of AlphaFold2 applications

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Protein homology model refinement by large-scale energy optimization

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Genomic language model predicts protein co-regulation and function

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Structure of a bd oxidase indicates similar mechanisms for membrane-integrated oxygen reductases

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Large-scale determination of previously unsolved protein structures using evolutionary information

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One- and Two-Particle Correlation Functions in the Cluster Perturbation Theory for Cuprates

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Magnetic Collapse in Fe3Se4 under High Pressure

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Quench dynamics and defects formation in the Ising chain in a transverse magnetic field

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Cyclic peptide structure prediction and design using AlphaFold2

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Computational design of constitutively active cGAS

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Pseudoscorpion mitochondria show rearranged genes and genome-wide reductions of RNA gene sizes and inferred structures, yet typical nucleotide composition bias

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Patterns and drivers of diatom diversity and abundance in the global ocean

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Electronic Structure and Minimal Models for Flat and Corrugated CuO Monolayers: An Ab Initio Study

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Effect of Multiplicity Fluctuation in Cobalt Ions on Crystal Structure, Magnetic and Electrical Properties of NdCoO3 and SmCoO3

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Four steps for revealing and adjusting the 3D structure of aptamers in solution by small-angle X-ray scattering and computer simulation

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