Sergey Ovchinnikov

Sergey Ovchinnikov

Irwin and Helen 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. Femtosecond Three-Dimensional Imaging of Single-Protein with Hard X-ray Laser. Xavier, PL, Morgan, AJ, Bielecki, J, Samanta, AK, Dold, S, Li, C, Gao, X, Passmore, SK, Kurta, RP, Berberich, TB et al.. 2026. ArXiv , .
    PMID:42926742
  2. Proteome-wide crosslinking mass spectrometry reveals novel components of essential complexes in Toxoplasma. Butterworth, S, Gin, AL, Shikha, S, Tengganu, I, Rush, J, Duraisingh, T, Sodeinde, V, Lemgruber, L, Schulte, F, Hu, K et al.. 2026. bioRxiv , .
    doi: 10.64898/2026.09.01.748362PMID:42922580
  3. Molecular fossils of an ancestral code revealed by large-scale analysis of tRNAs. Nova Royo, A, Martín-Cabezas, P, Ovchinnikov, S, Schimmel, P, Ribas de Pouplana, L. 2026. Proc Natl Acad Sci U S A 123, e2627541123.
    doi: 10.1073/pnas.2627541123PMID:42905541
  4. 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. Nature 658, 1077-1087.
    doi: 10.1038/s41586-026-10989-4PMID:42742167
  5. Systematic discovery of circular permutations across the protein universe using CIRPIN. Kolodziej, AR, Abulnaga, SM, Ovchinnikov, S. 2026. Proc Natl Acad Sci U S A 123, e2605178123.
    doi: 10.1073/pnas.2605178123PMID:42696540
  6. 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 189, 4964-4979.e8.
    doi: 10.1016/j.cell.2026.06.029PMID:42480528
  7. 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
  8. 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
  9. 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
  10. 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
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