Dauparas, Justas

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

Robust deep learning–based protein sequence design using ProteinMPNN

Dauparas, J., Anishchenko, I., Bennett, N., Bai, H., Ragotte, R. J., Milles, L. F., Wicky, B. I. M., Courbet, A., de Haas, R. J., Bethel, N., et al. (2022) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 2,210

Robust deep learning based protein sequence design using ProteinMPNN

Dauparas, J., Anishchenko, I., Bennett, N., Bai, H., Ragotte, R. J., Milles, L. F., Wicky, B. I. M., Courbet, A., de Haas, R. J., Bethel, N., et al. (2022) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 2,107

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

Improving de novo protein binder design with deep learning

Bennett, N. R., Coventry, B., Goreshnik, I., Huang, B., Allen, A., Vafeados, D., Peng, Y. P., Dauparas, J., Baek, M., Stewart, L., et al. (2023) · Nature Communications

Protein Structure and Dynamicsvaccines and immunoinformatics approaches

Cited by 402

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

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

Improving protein expression, stability, and function with ProteinMPNN

Sumida, K. H., Núñez-Franco, R., Kalvet, I., Pellock, S. J., Wicky, B. I. M., Milles, L. F., Dauparas, J., Wang, J., Kipnis, Y., Jameson, N., et al. (2023) · Journal of the American Chemical Society

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 344

Improved protein structure refinement guided by deep learning based accuracy estimation

Hiranuma, N., Park, H., Baek, M., Anishchenko, I., Dauparas, J., & Baker, D. (2021) · Nature Communications

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 243

Hallucinating symmetric protein assemblies

Wicky, B. I. M., Milles, L. F., Courbet, A., Ragotte, R. J., Dauparas, J., Kinfu, E., Tipps, S., Kibler, R. D., Baek, M., DiMaio, F., et al. (2022) · Science

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 240

Hallucinating protein assemblies

Wicky, B. I. M., Milles, L. F., Courbet, A., Ragotte, R. J., Dauparas, J., Kinfu, E., Tipps, S., Kibler, R. D., Baek, M., DiMaio, F., et al. (2022) · Science

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 240

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

Peptide-binding specificity prediction using fine-tuned protein structure prediction networks

Motmaen, A., Dauparas, J., Baek, M., Abedi, M. H., Baker, D., & Bradley, P. (2023) · Proceedings of the National Academy of Sciences

vaccines and immunoinformatics approachesProtein Structure and Dynamics

Cited by 124

Design of stimulus-responsive two-state hinge proteins

Praetorius, F., Leung, P. J. Y., Tessmer, M. H., Broerman, A., Demakis, C., Dishman, A. F., Pillai, A., Idris, A., Juergens, D., Dauparas, J., et al. (2023) · Science

Protein Structure and DynamicsBiochemical and Structural Characterization

Cited by 90

Design of stimulus-responsive two-state hinge proteins

Praetorius, F., Leung, P. J. Y., Tessmer, M. H., Broerman, A., Demakis, C., Dishman, A. F., Pillai, A., Idris, A., Juergens, D., Dauparas, J., et al. (2023) · Science

Protein Structure and DynamicsBiochemical and Structural Characterization

Cited by 90

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

Rapid and automated design of two-component protein nanomaterials using ProteinMPNN

de Haas, R. J., Brunette, N., Goodson, A., Dauparas, J., Yi, S. Y., Yang, E. C., Dowling, Q., Nguyen, H., Kang, A., Bera, A. K., et al. (2024) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsBiochemical and Structural Characterization

Cited by 42

Rapid and automated design of two-component protein nanomaterials using ProteinMPNN

de Haas, R. J., Brunette, N., Goodson, A., Dauparas, J., Yi, S. Y., Yang, E. C., Dowling, Q., Nguyen, H., Kang, A., Bera, A. K., et al. (2023) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsBiochemical and Structural Characterization

Cited by 42

Small-molecule binding and sensing with a designed protein family

Lee, G. R., Pellock, S. J., Norn, C., Tischer, D., Dauparas, J., Anischenko, I., Mercer, J. A. M., Kang, A., Bera, A., Nguyen, H., et al. (2023) · Nature Communications

Protein Structure and DynamicsBiochemical and Structural Characterization

Cited by 41

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

Computational design of bifaceted protein nanomaterials

Rankovic, S., Carr, K. D., Decarreau, J., Skotheim, R., Kibler, R. D., Ols, S., Lee, S., Chun, J.-H., Tooley, M. R., Dauparas, J., et al. (2025) · Nature Materials

Protein Structure and DynamicsSupramolecular Self-Assembly in Materials

Cited by 17

Hallucination of closed repeat proteins containing central pockets

An, L., Hicks, D. R., Zorine, D., Dauparas, J., Wicky, B. I. M., Milles, L. F., Courbet, A., Bera, A. K., Nguyen, H., Kang, A., et al. (2023) · Nature Structural & Molecular Biology

Protein Structure and DynamicsBiochemical and Structural Characterization

Cited by 15

Hallucination of closed repeat proteins containing central pockets

An, L., Hicks, D. R., Zorine, D., Dauparas, J., Wicky, B. I. M., Milles, L. F., Courbet, A., Bera, A. K., Nguyen, H., Kang, A., et al. (2022) · Nature Structural & Molecular Biology

Protein Structure and DynamicsBiochemical and Structural Characterization

Cited by 15