Ovchinnikov, Sergey

ColabFold - Making protein folding accessible to all

Mirdita, M., Schütze, K., Moriwaki, Y., Heo, L., Ovchinnikov, S., & Steinegger, M. (2021) · Nature Methods

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 9,391

Accurate prediction of protein structures and interactions using a 3-track network

Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G. R., Wang, J., Cong, Q., Kinch, L. N., Schaeffer, R. D., et al. (2021) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 5,549

De novo design of protein structure and function with RFdiffusion

Watson, J. L., Juergens, D., Bennett, N. R., Trippe, B. L., Yim, J., Eisenach, H. E., Ahern, W., Borst, A. J., Ragotte, R. J., Milles, L. F., et al. (2023) · Nature

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 2,325

Improved protein structure prediction using predicted interresidue orientations

Yang, J., Anishchenko, I., Park, H., Peng, Z., Ovchinnikov, S., & Baker, D. (2020) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 1,421

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Leman, J. K., Weitzner, B. D., Lewis, S. M., Adolf-Bryfogle, J., Alam, N., Alford, R. F., Aprahamian, M., Baker, D., Barlow, K. A., Barth, P., et al. (2020) · Nature Methods

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 888

A structural biology community assessment of AlphaFold2 applications

Akdel, M., Pires, D. E. V., Pardo, E. P., Jänes, J., Zalevsky, A. O., Mészáros, B., Bryant, P., Good, L. L., Laskowski, R. A., Pozzati, G., et al. (2022) · Nature Structural & Molecular Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 675

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

Ovchinnikov, S., Kamisetty, H., & Baker, D. (2014) · eLife

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 629

De novo protein design by deep network hallucination

Anishchenko, I., Chidyausiku, T. M., Ovchinnikov, S., Pellock, S. J., & Baker, D. (2020) · Nature

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 629

Predicting multiple conformations via sequence clustering and AlphaFold2

Wayment-Steele, H. K., Ojoawo, A., Otten, R., Apitz, J. M., Pitsawong, W., Hömberger, M., Ovchinnikov, S., Colwell, L., & Kern, D. (2024) · Nature

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 545

Computed structures of core eukaryotic protein complexes

Humphreys, I. R., Pei, J., Baek, M., Krishnakumar, A., Anishchenko, I., Ovchinnikov, S., Zhang, J., Ness, T. J., Banjade, S., Bagde, S. R., et al. (2021) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 542

Structures of core eukaryotic protein complexes

Humphreys, I. R., Pei, J., Baek, M., Krishnakumar, A., Anishchenko, I., Ovchinnikov, S., Zhang, J., Ness, T. J., Banjade, S., Bagde, S., et al. (2021) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 541

Protein structure determination using metagenome sequence data

Ovchinnikov, S., Park, H., Varghese, N., Huang, P.-S., Pavlopoulos, G. A., Kim, D. E., Kamisetty, H., Kyrpides, N. C., & Baker, D. (2017) · Science

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 520

Deep learning methods for designing proteins scaffolding functional sites

Wang, J., Lisanza, S., Juergens, D., Tischer, D., Anishchenko, I., Baek, M., Watson, J. L., Chun, J. H., Milles, L. F., Dauparas, J., et al. (2021) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 487

Scaffolding protein functional sites using deep learning

Wang, J., Lisanza, S., Juergens, D., Tischer, D., Watson, J. L., Castro, K. M., Ragotte, R., Saragovi, A., Milles, L. F., Baek, M., et al. (2022) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 487

Mega-scale experimental analysis of protein folding stability in biology and protein design

Tsuboyama, K., Dauparas, J., Chen, J., Laine, E., Mohseni Behbahani, Y., Weinstein, J. J., Mangan, N. M., Ovchinnikov, S., & Rocklin, G. J. (2022) · Nature

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 352

De novo design of a fluorescence-activating β-barrel

Dou, J., Vorobieva, A. A., Sheffler, W., Doyle, L. A., Park, H., Bick, M. J., Mao, B., Foight, G. W., Lee, M. Y., Gagnon, L. A., et al. (2018) · Nature

Protein Structure and DynamicsBiochemical and Structural Characterization

Cited by 351

Mega-scale experimental analysis of protein folding stability in biology and design

Tsuboyama, K., Dauparas, J., Chen, J., Laine, E., Mohseni Behbahani, Y., Weinstein, J. J., Mangan, N. M., Ovchinnikov, S., & Rocklin, G. J. (2023) · Nature

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 350

Transformer protein language models are unsupervised structure learners

Rao, R., Meier, J., Sercu, T., Ovchinnikov, S., & Rives, A. (2020) · bioRxiv (Cold Spring Harbor Laboratory)

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 341

State-of-the-art estimation of protein model accuracy using AlphaFold

Roney, J. P., & Ovchinnikov, S. (2022) · Physical Review Letters

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 281

State-of-the-Art Estimation of Protein Model Accuracy Using AlphaFold

Roney, J. P., & Ovchinnikov, S. (2022) · Physical Review Letters

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 281

Protein interaction networks revealed by proteome coevolution

Cong, Q., Anishchenko, I., Ovchinnikov, S., & Baker, D. (2019) · Science

Bioinformatics and Genomic NetworksProtein Structure and Dynamics

Cited by 241

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

Ovchinnikov, S., Kinch, L., Park, H., Liao, Y., Pei, J., Kim, D. E., Kamisetty, H., Grishin, N. V., & Baker, D. (2015) · eLife

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 222

Origins of coevolution between residues distant in protein 3D structures

Anishchenko, I., Ovchinnikov, S., Kamisetty, H., & Baker, D. (2017) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 185

Language models generalize beyond natural proteins

Verkuil, R., Kabeli, O., Du, Y., Wicky, B. I. M., Milles, L. F., Dauparas, J., Baker, D., Ovchinnikov, S., Sercu, T., & Rives, A. (2022) · bioRxiv (Cold Spring Harbor Laboratory)

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 181