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Sergey Ovchinnikov, Ph.D. - Publications

Affiliations: 
University of Washington, Seattle, Seattle, WA 
 2017- JHDSF Program Harvard University, Cambridge, MA, United States 
Website:
solab.org
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55 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Hwang Y, Cornman AL, Kellogg EH, Ovchinnikov S, Girguis PR. Genomic language model predicts protein co-regulation and function. Nature Communications. 15: 2880. PMID 38570504 DOI: 10.1038/s41467-024-46947-9  0.642
2024 Goverde CA, Pacesa M, Goldbach N, Dornfeld LJ, Balbi PEM, Georgeon S, Rosset S, Kapoor S, Choudhury J, Dauparas J, Schellhaas C, Kozlov S, Baker D, Ovchinnikov S, Vecchio AJ, et al. Computational design of soluble functional analogues of integral membrane proteins. Biorxiv : the Preprint Server For Biology. PMID 38496615 DOI: 10.1101/2023.05.09.540044  0.422
2024 Schweke H, Pacesa M, Levin T, Goverde CA, Kumar P, Duhoo Y, Dornfeld LJ, Dubreuil B, Georgeon S, Ovchinnikov S, Woolfson DN, Correia BE, Dey S, Levy ED. An atlas of protein homo-oligomerization across domains of life. Cell. 187: 999-1010.e15. PMID 38325366 DOI: 10.1016/j.cell.2024.01.022  0.307
2023 Pavlopoulos GA, Baltoumas FA, Liu S, Selvitopi O, Camargo AP, Nayfach S, Azad A, Roux S, Call L, Ivanova NN, Chen IM, Paez-Espino D, Karatzas E, Iliopoulos I, Konstantinidis K, ... ... Ovchinnikov S, et al. Unraveling the functional dark matter through global metagenomics. Nature. 622: 594-602. PMID 37821698 DOI: 10.1038/s41586-023-06583-7  0.66
2023 Baltoumas FA, Karatzas E, Liu S, Ovchinnikov S, Sofianatos Y, Chen IM, Kyrpides NC, Pavlopoulos GA. NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes. Nucleic Acids Research. PMID 37811892 DOI: 10.1093/nar/gkad800  0.644
2023 Tsuboyama K, Dauparas J, Chen J, Laine E, Mohseni Behbahani Y, Weinstein JJ, Mangan NM, Ovchinnikov S, Rocklin GJ. Mega-scale experimental analysis of protein folding stability in biology and design. Nature. PMID 37468638 DOI: 10.1038/s41586-023-06328-6  0.754
2023 Watson JL, Juergens D, Bennett NR, Trippe BL, Yim J, Eisenach HE, Ahern W, Borst AJ, Ragotte RJ, Milles LF, Wicky BIM, Hanikel N, Pellock SJ, Courbet A, Sheffler W, ... ... Ovchinnikov S, et al. De novo design of protein structure and function with RFdiffusion. Nature. PMID 37433327 DOI: 10.1038/s41586-023-06415-8  0.755
2023 Baltoumas FA, Karatzas E, Paez-Espino D, Venetsianou NK, Aplakidou E, Oulas A, Finn RD, Ovchinnikov S, Pafilis E, Kyrpides NC, Pavlopoulos GA. Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters. Frontiers in Bioinformatics. 3: 1157956. PMID 36959975 DOI: 10.3389/fbinf.2023.1157956  0.303
2023 Kim DE, Jensen DR, Feldman D, Tischer D, Saleem A, Chow CM, Li X, Carter L, Milles L, Nguyen H, Kang A, Bera AK, Peterson FC, Volkman BF, Ovchinnikov S, et al. De novo design of small beta barrel proteins. Proceedings of the National Academy of Sciences of the United States of America. 120: e2207974120. PMID 36897987 DOI: 10.1073/pnas.2207974120  0.423
2023 Rettie SA, Campbell KV, Bera AK, Kang A, Kozlov S, De La Cruz J, Adebomi V, Zhou G, DiMaio F, Ovchinnikov S, Bhardwaj G. Cyclic peptide structure prediction and design using AlphaFold. Biorxiv : the Preprint Server For Biology. PMID 36865323 DOI: 10.1101/2023.02.25.529956  0.776
2023 Dowling QM, Volkman HE, Gray EE, Ovchinnikov S, Cambier S, Bera AK, Sankaran B, Johnson MR, Bick MJ, Kang A, Stetson DB, King NP. Computational design of constitutively active cGAS. Nature Structural & Molecular Biology. PMID 36593311 DOI: 10.1038/s41594-022-00862-z  0.291
2023 Cheng Y, Wang H, Xu H, Liu Y, Ma B, Chen X, Zeng X, Wang X, Wang B, Shiau C, Ovchinnikov S, Su XD, Wang C. Co-evolution-based prediction of metal-binding sites in proteomes by machine learning. Nature Chemical Biology. PMID 36593274 DOI: 10.1038/s41589-022-01223-z  0.631
2022 Roney JP, Ovchinnikov S. State-of-the-Art Estimation of Protein Model Accuracy Using AlphaFold. Physical Review Letters. 129: 238101. PMID 36563190 DOI: 10.1103/PhysRevLett.129.238101  0.425
2022 Petti S, Bhattacharya N, Rao R, Dauparas J, Thomas N, Zhou J, Rush AM, Koo P, Ovchinnikov S. End-to-end learning of multiple sequence alignments with differentiable Smith-Waterman. Bioinformatics (Oxford, England). PMID 36355460 DOI: 10.1093/bioinformatics/btac724  0.351
2022 Akdel M, Pires DEV, Pardo EP, Jänes J, Zalevsky AO, Mészáros B, Bryant P, Good LL, Laskowski RA, Pozzati G, Shenoy A, Zhu W, Kundrotas P, Serra VR, Rodrigues CHM, ... ... Ovchinnikov S, et al. A structural biology community assessment of AlphaFold2 applications. Nature Structural & Molecular Biology. PMID 36344848 DOI: 10.1038/s41594-022-00849-w  0.482
2022 Wang J, Lisanza S, Juergens D, Tischer D, Watson JL, Castro KM, Ragotte R, Saragovi A, Milles LF, Baek M, Anishchenko I, Yang W, Hicks DR, Expòsit M, Schlichthaerle T, ... ... Ovchinnikov S, et al. Scaffolding protein functional sites using deep learning. Science (New York, N.Y.). 377: 387-394. PMID 35862514 DOI: 10.1126/science.abn2100  0.563
2022 Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M. ColabFold: making protein folding accessible to all. Nature Methods. 19: 679-682. PMID 35637307 DOI: 10.1038/s41592-022-01488-1  0.45
2022 Bhattacharya N, Thomas N, Rao R, Dauparas J, Koo PK, Baker D, Song YS, Ovchinnikov S. Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 27: 34-45. PMID 34890134  0.499
2021 Anishchenko I, Pellock SJ, Chidyausiku TM, Ramelot TA, Ovchinnikov S, Hao J, Bafna K, Norn C, Kang A, Bera AK, DiMaio F, Carter L, Chow CM, Montelione GT, Baker D. De novo protein design by deep network hallucination. Nature. PMID 34853475 DOI: 10.1038/s41586-021-04184-w  0.52
2021 Humphreys IR, Pei J, Baek M, Krishnakumar A, Anishchenko I, Ovchinnikov S, Zhang J, Ness TJ, Banjade S, Bagde SR, Stancheva VG, Li XH, Liu K, Zheng Z, Barrero DJ, et al. Computed structures of core eukaryotic protein complexes. Science (New York, N.Y.). eabm4805. PMID 34762488 DOI: 10.1126/science.abm4805  0.432
2021 Ovchinnikov S, Huang PS. Structure-based protein design with deep learning. Current Opinion in Chemical Biology. 65: 136-144. PMID 34547592 DOI: 10.1016/j.cbpa.2021.08.004  0.637
2021 Baek M, DiMaio F, Anishchenko I, Dauparas J, Ovchinnikov S, Lee GR, Wang J, Cong Q, Kinch LN, Schaeffer RD, Millán C, Park H, Adams C, Glassman CR, DeGiovanni A, et al. Accurate prediction of protein structures and interactions using a three-track neural network. Science (New York, N.Y.). PMID 34282049 DOI: 10.1126/science.abj8754  0.51
2021 Norn C, Wicky BIM, Juergens D, Liu S, Kim D, Tischer D, Koepnick B, Anishchenko I, Baker D, Ovchinnikov S. Protein sequence design by conformational landscape optimization. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33712545 DOI: 10.1073/pnas.2017228118  0.702
2020 Agbleke AA, Amitai A, Buenrostro JD, Chakrabarti A, Chu L, Hansen AS, Koenig KM, Labade AS, Liu S, Nozaki T, Ovchinnikov S, Seeber A, Shaban HA, Spille JH, Stephens AD, et al. Advances in Chromatin and Chromosome Research: Perspectives from Multiple Fields. Molecular Cell. PMID 32768408 DOI: 10.1016/J.Molcel.2020.07.003  0.633
2020 Cooper CJ, Zheng K, Rush KW, Johs A, Sanders BC, Pavlopoulos GA, Kyrpides NC, Podar M, Ovchinnikov S, Ragsdale SW, Parks JM. Structure determination of the HgcAB complex using metagenome sequence data: insights into microbial mercury methylation. Communications Biology. 3: 320. PMID 32561885 DOI: 10.1038/s42003-020-1047-5  0.345
2020 Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, ... ... Ovchinnikov S, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2  0.562
2020 Wu X, Siggel M, Ovchinnikov S, Mi W, Svetlov V, Nudler E, Liao M, Hummer G, Rapoport TA. Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex. Science (New York, N.Y.). 368. PMID 32327568 DOI: 10.1126/Science.Aaz2449  0.304
2020 Yang J, Anishchenko I, Park H, Peng Z, Ovchinnikov S, Baker D. Improved protein structure prediction using predicted interresidue orientations. Proceedings of the National Academy of Sciences of the United States of America. PMID 31896580 DOI: 10.1073/Pnas.1914677117  0.611
2019 Porter KA, Padhorny D, Desta I, Ignatov M, Beglov D, Kotelnikov S, Sun Z, Alekseenko A, Anishchenko I, Cong Q, Ovchinnikov S, Baker D, Vajda S, Kozakov D. Template-Based Modeling by ClusPro in CASP13 and the Potential for Using Co-evolutionary Information in Docking. Proteins. PMID 31444975 DOI: 10.1002/Prot.25808  0.568
2019 Cong Q, Anishchenko I, Ovchinnikov S, Baker D. Protein interaction networks revealed by proteome coevolution. Science (New York, N.Y.). 365: 185-189. PMID 31296772 DOI: 10.1126/Science.Aaw6718  0.537
2019 Li D, Ma Y, Zhou Y, Gou J, Zhong Y, Zhao L, Han L, Ovchinnikov S, Ma L, Huang S, Greisen P, Shang Y. A structural and data-driven approach to engineering a plant cytochrome P450 enzyme. Science China. Life Sciences. PMID 31119558 DOI: 10.1007/S11427-019-9538-3  0.42
2019 Zhang L, Shen H, Gong Y, Pang X, Yi M, Guo L, Li J, Arroyo S, Lu X, Ovchinnikov S, Cheng G, Liu X, Jiang X, Feng S, Deng H. Development of a dual-functional conjugate of antigenic peptide and Fc-III mimetics (DCAF) for targeted antibody blocking. Chemical Science. 10: 3271-3280. PMID 30996912 DOI: 10.1039/C8Sc05273E  0.519
2018 Dou J, Vorobieva AA, Sheffler W, Doyle LA, Park H, Bick MJ, Mao B, Foight GW, Lee MY, Gagnon LA, Carter L, Sankaran B, Ovchinnikov S, Marcos E, Huang PS, et al. De novo design of a fluorescence-activating β-barrel. Nature. PMID 30209393 DOI: 10.1038/S41586-018-0509-0  0.753
2018 Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, ... ... Ovchinnikov S, et al. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Scientific Reports. 8: 9939. PMID 29967418 DOI: 10.1038/s41598-018-26812-8  0.756
2018 Sutherland MC, Jarodsky JM, Ovchinnikov S, Baker D, Kranz RG. Structurally Mapping Endogenous Heme in the CcmCDE Membrane Complex for Cytochrome c Biogenesis. Journal of Molecular Biology. PMID 29518410 DOI: 10.1016/J.Jmb.2018.01.022  0.419
2018 Park H, Ovchinnikov S, Kim DE, DiMaio F, Baker D. Protein homology model refinement by large-scale energy optimization. Proceedings of the National Academy of Sciences of the United States of America. PMID 29507254 DOI: 10.1073/Pnas.1719115115  0.481
2017 Ovchinnikov S, Park H, Kim D, DiMaio F, Baker D. Protein structure prediction using Rosetta in CASP12. Proteins. PMID 28940798 DOI: 10.1002/Prot.25390  0.539
2017 Park H, Kim D, Ovchinnikov S, Baker D, DiMaio F. Automatic structure prediction of oligomeric assemblies using Robetta in CASP12. Proteins. PMID 28913931 DOI: 10.1002/Prot.25387  0.51
2017 Anishchenko I, Ovchinnikov S, Kamisetty H, Baker D. Origins of coevolution between residues distant in protein 3D structures. Proceedings of the National Academy of Sciences of the United States of America. PMID 28784799 DOI: 10.1073/Pnas.1702664114  0.482
2017 Schoebel S, Mi W, Stein A, Ovchinnikov S, Pavlovicz R, DiMaio F, Baker D, Chambers MG, Su H, Li D, Rapoport TA, Liao M. Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3. Nature. PMID 28682307 DOI: 10.1038/Nature23314  0.381
2017 Simkovic F, Ovchinnikov S, Baker D, Rigden DJ. Applications of contact predictions to structural biology. Iucrj. 4: 291-300. PMID 28512576 DOI: 10.1107/S2052252517005115  0.514
2017 Goldsmith M, Aggarwal N, Ashani Y, Jubran H, Greisen PJ, Ovchinnikov S, Leader H, Baker D, Sussman JL, Goldenzweig A, Fleishman SJ, Tawfik DS. Overcoming an optimization plateau in the directed evolution of highly efficient nerve agent bioscavengers. Protein Engineering, Design & Selection : Peds. 1-13. PMID 28159998 DOI: 10.1093/Protein/Gzx003  0.37
2017 Ovchinnikov S, Park H, Varghese N, Huang PS, Pavlopoulos GA, Kim DE, Kamisetty H, Kyrpides NC, Baker D. Protein structure determination using metagenome sequence data. Science (New York, N.Y.). 355: 294-298. PMID 28104891 DOI: 10.1126/Science.Aah4043  0.646
2016 DaRosa PA, Ovchinnikov S, Xu W, Klevit RE. Structural insights into SAM domain-mediated tankyrase oligomerization. Protein Science : a Publication of the Protein Society. PMID 27328430 DOI: 10.1002/Pro.2968  0.355
2016 Ovchinnikov S, Park H, Kim DE, Liu Y, Yu-Ruei Wang R, Baker D. Structure Prediction using sparse simulated NOE restraints with Rosetta in CASP11. Proteins. PMID 26857542 DOI: 10.1002/Prot.25006  0.542
2015 Ovchinnikov S, Kim DE, Wang RY, Liu Y, DiMaio F, Baker D. Improved de novo structure prediction in CASP11 by incorporating Co-evolution information into rosetta. Proteins. PMID 26677056 DOI: 10.1002/Prot.24974  0.699
2015 Goldsmith M, Eckstein S, Ashani Y, Greisen P, Leader H, Sussman JL, Aggarwal N, Ovchinnikov S, Tawfik DS, Baker D, Thiermann H, Worek F. Catalytic efficiencies of directly evolved phosphotriesterase variants with structurally different organophosphorus compounds in vitro. Archives of Toxicology. PMID 26612364 DOI: 10.1007/S00204-015-1626-2  0.374
2015 Ovchinnikov S, Kinch L, Park H, Liao Y, Pei J, Kim DE, Kamisetty H, Grishin NV, Baker D. Large scale determination of previously unsolved protein structures using evolutionary information. Elife. 4. PMID 26335199 DOI: 10.7554/Elife.09248  0.539
2015 Antala S, Ovchinnikov S, Kamisetty H, Baker D, Dempski RE. Computational modeling and functional studies provide a structural scaffold for the zinc transporter hZIP4. The Journal of Biological Chemistry. PMID 25971965 DOI: 10.1074/Jbc.M114.617613  0.513
2015 Ovchinnikov S, Kinch L, Park H, Liao Y, Pei J, Kim DE, Kamisetty H, Grishin NV, Baker D. Author response: Large-scale determination of previously unsolved protein structures using evolutionary information Elife. DOI: 10.7554/Elife.09248.031  0.419
2014 Ovchinnikov S, Kamisetty H, Baker D. Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information. Elife. 3: e02030. PMID 24842992 DOI: 10.7554/Elife.02030  0.514
2014 Ovchinnikov S, Kamisetty H, Baker D. Author response: Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information Elife. DOI: 10.7554/Elife.02030.014  0.439
2014 Ovchinnikov S, Kamisetty H, Baker D. Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information Elife. 2014. DOI: 10.7554/eLife.02030  0.373
2013 Kamisetty H, Ovchinnikov S, Baker D. Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era Proceedings of the National Academy of Sciences of the United States of America. 110: 15674-15679. PMID 24009338 DOI: 10.1073/Pnas.1314045110  0.527
2012 Ovchinnikov S, Masta SE. Pseudoscorpion mitochondria show rearranged genes and genome-wide reductions of RNA gene sizes and inferred structures, yet typical nucleotide composition bias. Bmc Evolutionary Biology. 12: 31. PMID 22409411 DOI: 10.1186/1471-2148-12-31  0.343
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