Ovchinnikov, Sergey

An atlas of protein homo-oligomerization across domains of life

Schweke, H., Levin, T., Pacesa, M., Goverde, C. A., Kumar, P., Duhoo, Y., Dornfeld, L. J., Dubreuil, B., Georgeon, S., Ovchinnikov, S., et al. (2023) · Cell

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 144

An atlas of protein homo-oligomerization across domains of life

Schweke, H., Pacesa, M., Levin, T., Goverde, C. A., Kumar, P., Duhoo, Y., Dornfeld, L. J., Dubreuil, B., Georgeon, S., Ovchinnikov, S., et al. (2024) · Cell

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 144

Protein sequence design by conformational landscape optimization

Norn, C., Wicky, B. I. M., Juergens, D., Liu, S., Kim, D., Tischer, D., Koepnick, B., Anishchenko, I., Players, F., Baker, D., et al. (2021) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 144

Protein language models learn evolutionary statistics of interacting sequence motifs

Zhang, Z., Wayment-Steele, H. K., Brixi, G., Wang, H., Kern, D., & Ovchinnikov, S. (2024) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 140

A structural biology community assessment of AlphaFold 2 applications

Akdel, M., Pires, D. E. V., Porta Pardo, E., Jänes, J., Zalevsky, A. O., Mészáros, B., Bryant, P., Good, L. L., Laskowski, R. A., Pozzati, G., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory)

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 122

Genomic language model predicts protein co-regulation and function

Hwang, Y., Cornman, A. L., Kellogg, E. H., Ovchinnikov, S., & Girguis, P. R. (2024) · Nature Communications

Genomics and Phylogenetic StudiesMachine Learning in Bioinformatics

Cited by 99

Genomic language model predicts protein co-regulation and function

Hwang, Y., Cornman, A. L., Kellogg, E. H., Ovchinnikov, S., & Girguis, P. R. (2023) · Nature Communications

Genomics and Phylogenetic StudiesMachine Learning in Bioinformatics

Cited by 98

Structure-based protein design with deep learning

Ovchinnikov, S., & Huang, P.-S. (2021) · Current Opinion in Chemical Biology

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 93

End-to-end learning of multiple sequence alignments with differentiable Smith–Waterman

Petti, S., Bhattacharya, N., Rao, R., Dauparas, J., Thomas, N., Zhou, J., Rush, A. M., Koo, P., & Ovchinnikov, S. (2023) · Bioinformatics

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 54

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. (2026) · Nature Biotechnology

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 35

Structurally Mapping Endogenous Heme in the CcmCDE Membrane Complex for Cytochrome c Biogenesis

Sutherland, M. C., Jarodsky, J. M., Ovchinnikov, S., Baker, D., & Kranz, R. G. (2018) · Journal of Molecular Biology

Metalloenzymes and iron-sulfur proteinsEnzyme Structure and Function

Cited by 23

Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention

Bhattacharya, N., Thomas, N., Rao, R., Dauparas, J., Koo, P. K., Baker, D., Song, Y. S., & Ovchinnikov, S. (2021) · Biocomputing 2022

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 20

Designing Novel Solenoid Proteins with In Silico Evolution

Pretorius, D., Nikov, G. I., Washio, K., Florent, S.-W., Taunt, H. N., Ovchinnikov, S., & Murray, J. W. (2025) · Communications Chemistry

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 10

Does sequence clustering confound AlphaFold2?

Wayment-Steele, H. K., Ovchinnikov, S., Colwell, L., & Kern, D. (2024) · Journal of Molecular Biology

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 8