Baker, David

Bond-centric modular design of protein assemblies

Wang, S., Favor, A., Kibler, R. D., Lubner, J. M., Borst, A. J., Coudray, N., Redler, R., Chiang, H. T., Sheffler, W., Hsia, Y., et al. (2024) · Nature Materials

Supramolecular Self-Assembly in MaterialsBiochemical and Structural Characterization

Cited by 22

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

Rapid and accurate prediction of protein homo-oligomer symmetry with Seq2Symm

Kshirsagar, M., Meller, A., Humphreys, I., Sledzieski, S., Xu, Y., Dodhia, R., Horvitz, E., Berger, B., Bowman, G., Ferres, J. L., et al. (2024) · Nature Communications

Protein Structure and DynamicsMachine Learning in Bioinformatics

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

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

Protein oligomer modeling guided by predicted interchain contacts in CASP14

Baek, M., Anishchenko, I., Park, H., Humphreys, I. R., & Baker, D. (2021) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 18

Local structural flexibility drives oligomorphism in computationally designed protein assemblies

Khmelinskaia, A., Bethel, N. P., Fatehi, F., Antanasijevic, A., Borst, A. J., Lai, S.-H., Wang, J. Y. (., Mallik, B. B., Miranda, M. C., Watkins, A. M., et al. (2023) · Nature Structural & Molecular Biology

Protein Structure and DynamicsBiochemical and Structural Characterization

Cited by 18

Local structural flexibility drives oligomorphism in computationally designed protein assemblies

Khmelinskaia, A., Bethel, N. P., Fatehi, F., Mallik, B. B., Antanasijevic, A., Borst, A. J., Lai, S.-H., Chim, H. Y., Wang, J. Y. ‘., Miranda, M. C., et al. (2025) · Nature Structural & Molecular Biology

Protein Structure and DynamicsBiochemical and Structural Characterization

Cited by 18

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

Computational design of serine hydrolases

Lauko, A., Pellock, S. J., Anischanka, I., Sumida, K. H., Juergens, D., Ahern, W., Shida, A., Hunt, A., Kalvet, I., Norn, C., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory)

Protein Structure and DynamicsEnzyme Catalysis and Immobilization

Cited by 16

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

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

De novo design of Ras isoform selective binders

Zhang, J. Z., Li, X., Batingana, A. R., Liu, C., Jiang, H., Shannon, K., Huang, B. J., Wu, K., & Baker, D. (2026) · Cell Chemical Biology

Protein Kinase Regulation and GTPase SignalingComputational Drug Discovery Methods

Cited by 12

Inhibition of ice recrystallization with designed twistless helical repeat proteins

de Haas, R. J., Pyles, H., Huddy, T. F., van Ossenbruggen, J., Zheng, C., van den Broek, D., Carr, A., Bera, A. K., Kang, A., Brackenbrough, E., et al. (2025) · Proceedings of the National Academy of Sciences

Protein Structure and Dynamicsnanoparticles nucleation surface interactions

Cited by 6

Inhibition of ice recrystallization with designed twistless helical repeat proteins

de Haas, R. J., Pyles, H., Huddy, E. B., van Ossenbruggen, J., Zheng, C., van den Broek, D., Giezen, S. N., Carr, A., Bera, A. K., Kang, A., et al. (2025) · Proceedings of the National Academy of Sciences

Protein Structure and Dynamicsnanoparticles nucleation surface interactions

Cited by 6