Watson, Joseph L.

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

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

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

Diffusing protein binders to intrinsically disordered proteins

Liu, C., Wu, K., Choi, H., Han, H. L., Zhang, X., Watson, J. L., Ahn, G., Zhang, J. Z., Shijo, S., Good, L. L., et al. (2025) · Nature

Protein Structure and DynamicsChemical Synthesis and Analysis

Cited by 79

Synthetic Par polarity induces cytoskeleton asymmetry in unpolarized mammalian cells

Watson, J. L., Krüger, L. K., Ben-Sasson, A. J., Bittleston, A., Shahbazi, M. N., Planelles-Herrero, V. J., Chambers, J. E., Manton, J. D., Baker, D., & Derivery, E. (2023) · Cell

Microtubule and mitosis dynamicsDevelopmental Biology and Gene Regulation

Cited by 32

Diffusing protein binders to intrinsically disordered proteins

Liu, C., Wu, K., Choi, H., Han, H., Zhang, X., Watson, J. L., Shijo, S., Bera, A. K., Kang, A., Brackenbrough, E., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory)

Protein Structure and DynamicsChemical Synthesis and Analysis

Cited by 24

De novo design of high-affinity protein binders to bioactive helical peptides

Vázquez Torres, S., Leung, P. J. Y., Lutz, I. D., Venkatesh, P., Watson, J. L., Hink, F., Huynh, H.-H., Yeh, A. H.-W., Juergens, D., Bennett, N. R., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory)

Protein Structure and DynamicsChemical Synthesis and Analysis

Cited by 22

Parametrically guided design of beta barrels and transmembrane nanopores using deep learning

Kim, D. E., Watson, J. L., Juergens, D., Majumder, S., Sonigra, R., Gerben, S. R., Kang, A., Bera, A. K., Li, X., & Baker, D. (2024) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsNanopore and Nanochannel Transport Studies

Cited by 21

Parametrically guided design of beta barrels and transmembrane nanopores using deep learning

Kim, D. E., Watson, J. L., Juergens, D., Majumder, S., Sonigra, R., Gerben, S. R., Kang, A., Bera, A. K., Li, X., & Baker, D. (2025) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsNanopore and Nanochannel Transport Studies

Cited by 21

Accurate single-domain scaffolding of three nonoverlapping protein epitopes using deep learning

Castro, K. M., Watson, J. L., Wang, J., Southern, J., Ayardulabi, R., Georgeon, S., Rosset, S., Baker, D., & Correia, B. E. (2026) · Nature Chemical Biology

Protein Structure and Dynamicsvaccines and immunoinformatics approaches

Cited by 13