Wicky, Basile I. M.

Broadly applicable and accurate protein design by integrating structure prediction networks and diffusion generative models

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. (2022) · Nature

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 2,369

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

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

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 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

Atomically accurate de novo design of antibodies with RFdiffusion

Bennett, N. R., Watson, J. L., Ragotte, R. J., Borst, A. J., See, D. L., Weidle, C., Biswas, R., Yu, Y., Shrock, E. L., Ault, R., et al. (2024) · Nature

Monoclonal and Polyclonal Antibodies ResearchProtein Structure and Dynamics

Cited by 324

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

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

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