Sergey Ovchinnikov

Sergey Ovchinnikov

Helen and Irwin Sizer Career Development Professor

Sergey Ovchinnikov studies protein structure and evolution at environmental, organismal, genomic, structural, and molecular scales.

68-533A

Office

so3@mit.edu

Email

Building 68 - Koch Biology Building

Location

Lab Website
Martha Pham

Assistant

617-258-7851

Assistant Phone

Education

  • Graduate: PhD, 2017, University of Washington
  • Undergraduate: BS, 2010, Micro/Molecular Biology, Portland State University

Research Summary

Sergey Ovchinnikov uses phylogenetic inference, protein structure prediction/determination, protein design, deep learning, energy-based models, and differentiable programming to tackle evolutionary questions at environmental, organismal, genomic, structural, and molecular scales, with the aim of developing a unified model of protein evolution.

Recent Publications

  1. Expanding the scope of protein language modeling to protein-protein interactions with MSA Pairformer. Akiyama, Y, Zhang, Z, Tang, O, Kim, RS, Mirdita, M, Steinegger, M, Ovchinnikov, S. 2026. Cell , .
    doi: 10.1016/j.cell.2026.06.029PMID:42480528
  2. Learning millisecond protein dynamics from what is missing in NMR spectra. Wayment-Steele, HK, El Nesr, G, Hettiarachchi, R, Ojoawo, AM, Kariyawasam, H, Ovchinnikov, S, Kern, D. 2026. bioRxiv , .
    doi: 10.1101/2025.03.19.642801PMID:42427544
  3. Accurate protein stability prediction for small domains using mega-scale experiments. Cho, Y, Tsuboyama, K, Litberg, TJ, Jung, MD, Obisesan, A, Wang, Q, Phoumyvong, CM, Thibeault, J, Ovchinnikov, S, Rocklin, GJ et al.. 2026. bioRxiv , .
    doi: 10.64898/2026.05.19.726285PMID:42239239
  4. Toward life with a 19-amino acid alphabet through generative artificial intelligence design. Liu, L, Rochereau, C, Kozlov, S, Urtecho, G, Liu, X, Zhao, J, Wang, J, Huang, Y, Qu, Y, Zhang, Z et al.. 2026. Science 392, eaeb5171.
    doi: 10.1126/science.aeb5171PMID:42060756
  5. AF2BIND: predicting small-molecule binding sites using the pair representation of AlphaFold2. Gazizov, A, Lian, A, Goverde, C, Mou, J, Ovchinnikov, S, Polizzi, NF. 2026. Nat Methods 23, 626-635.
    doi: 10.1038/s41592-026-03011-2PMID:41814061
  6. Stable de novo protein design via joint conformational landscape and sequence optimization. Cho, Y, Dauparas, J, Tsuboyama, K, Rocklin, GJ, Ovchinnikov, S. 2025. Nat Commun 17, 8.
    doi: 10.1038/s41467-025-66526-wPMID:41444215
  7. Designing novel solenoid proteins with in silico evolution. Pretorius, D, Nikov, GI, Washio, K, Florent, SW, Taunt, HN, Ovchinnikov, S, Murray, JW. 2025. Commun Chem 9, 10.
    doi: 10.1038/s42004-025-01817-3PMID:41345299
  8. CIRPIN: Learning Circular Permutation-Invariant Representations to Uncover Putative Protein Homologs. Kolodziej, AR, Abulnaga, SM, Ovchinnikov, S. 2025. bioRxiv , .
    doi: 10.1101/2025.11.18.689110PMID:41332582
  9. Democratizing protein language model training, sharing and collaboration. Su, J, Li, Z, Tao, T, Han, C, He, Y, Dai, F, Yuan, Q, Gao, Y, Si, T, Zhang, X et al.. 2025. Nat Biotechnol , .
    doi: 10.1038/s41587-025-02859-7PMID:41136773
  10. One-shot design of functional protein binders with BindCraft. Pacesa, M, Nickel, L, Schellhaas, C, Schmidt, J, Pyatova, E, Kissling, L, Barendse, P, Choudhury, J, Kapoor, S, Alcaraz-Serna, A et al.. 2025. Nature 646, 483-492.
    doi: 10.1038/s41586-025-09429-6PMID:40866699
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