Baker, David

Cryo‐EM model validation using independent map reconstructions

DiMaio, F., Zhang, J., Chiu, W., & Baker, D. (2013) · Protein Science

Advanced Electron Microscopy Techniques and ApplicationsEnzyme Structure and Function

Cited by 72

De novo design of modular protein hydrogels with programmable intra- and extracellular viscoelasticity

Mout, R., Bretherton, R. C., Decarreau, J., Lee, S., Edman, N. I., Ahlrichs, M., Hsia, Y., Sahtoe, D. D., Ueda, G., Gregorio, N., et al. (2023) · Proceedings of the National Academy of Sciences

Supramolecular Self-Assembly in MaterialsHydrogels: synthesis, properties, applications

Cited by 61

Computational design of sequence-specific DNA-binding proteins

Glasscock, C. J., Pecoraro, R. J., McHugh, R., Doyle, L. A., Chen, W., Boivin, O., Lonnquist, B., Na, E., Politanska, Y., Haddox, H. K., et al. (2025) · Nature Structural & Molecular Biology

Protein Structure and DynamicsCRISPR and Genetic Engineering

Cited by 58

Computational design of closely related proteins that adopt two well-defined but structurally divergent folds

Wei, K. Y., Moschidi, D., Bick, M. J., Nerli, S., McShan, A. C., Carter, L. P., Huang, P.-S., Fletcher, D. A., Sgourakis, N. G., Boyken, S. E., et al. (2020) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsChemical Synthesis and Analysis

Cited by 57

Design of amyloidogenic peptide traps

Sahtoe, D. D., Andrzejewska, E. A., Han, H. L., Rennella, E., Schneider, M. M., Meisl, G., Ahlrichs, M., Decarreau, J., Nguyen, H., Kang, A., et al. (2024) · Nature Chemical Biology

Alzheimer's disease research and treatmentsProtein Structure and Dynamics

Cited by 48

Design of amyloidogenic peptide traps

Sahtoe, D. D., Andrzejewska, E. A., Han, H. L., Rennella, E., Schneider, M. M., Meisl, G., Ahlrichs, M., Decarreau, J., Nguyen, H., Kang, A., et al. (2023) · Nature Chemical Biology

Alzheimer's disease research and treatmentsProtein Structure and Dynamics

Cited by 48

The ΦPA3 Phage Nucleus is Enclosed by a Self-Assembling, 2D Crystalline Lattice

Nieweglowska, E., Brilot, A., Méndez-Moran, M., Baek, M., Li, J., Kokontis, C., Cheng, Y., Baker, D., Bondy-Denomy, J., & Agard, D. (2022) · Nature Communications

Bacteriophages and microbial interactionsAdvanced Electron Microscopy Techniques and Applications

Cited by 45

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

Computationally designed sensors for endogenous Ras activity reveal signaling effectors within oncogenic granules

Zhang, J. Z., Nguyen, W. H., Greenwood, N., Rose, J. C., Ong, S.-E., Maly, D. J., & Baker, D. (2022) · Nature Biotechnology

Protein Kinase Regulation and GTPase SignalingAdvanced Fluorescence Microscopy Techniques

Cited by 37

Computationally designed sensors detect endogenous Ras activity and signaling effectors at subcellular resolution

Zhang, J. Z., Nguyen, W. H., Greenwood, N., Rose, J. C., Ong, S.-E., Maly, D. J., & Baker, D. (2024) · Nature Biotechnology

Protein Kinase Regulation and GTPase SignalingAdvanced Fluorescence Microscopy Techniques

Cited by 37

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

De novo design and evolution of an artificial metathase for cytoplasmic olefin metathesis

Zou, Z., Kalvet, I., Lozhkin, B., Morris, E., Zhang, K., Chen, D., Ernst, M. L., Zhang, X., Baker, D., & Ward, T. R. (2025) · Nature Catalysis

Synthetic Organic Chemistry MethodsEnzyme Catalysis and Immobilization

Cited by 30

Computational Stabilization of a Non‐Heme Iron Enzyme Enables Efficient Evolution of New Function

King, B. R., Sumida, K. H., Caruso, J. L., Baker, D., & Zalatan, J. G. (2025) · Angewandte Chemie International Edition

Enzyme Catalysis and ImmobilizationProtein Structure and Dynamics

Cited by 26

ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models

Vallat, B., Tauriello, G., Bienert, S., Haas, J., Webb, B. M., Žídek, A., Zheng, W., Peisach, E., Piehl, D. W., Anischanka, I., et al. (2023) · Journal of Molecular Biology

Enzyme Structure and FunctionProtein Structure and Dynamics

Cited by 26

Characterizing and explaining impact of disease-associated mutations in proteins without known structures or structural homologues

Sen, N., Anishchenko, I., Bordin, N., Sillitoe, I., Velankar, S., Baker, D., & Orengo, C. (2021) · Briefings in Bioinformatics

Protein Structure and DynamicsGenomics and Rare Diseases

Cited by 25

Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs

Sen, N., Anishchenko, I., Bordin, N., Sillitoe, I., Velankar, S., Baker, D., & Orengo, C. (2022) · Briefings in Bioinformatics

Protein Structure and DynamicsGenomics and Rare Diseases

Cited by 25

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

Tuning insulin receptor signaling using de novo-designed agonists

Wang, X., Cardoso, S., Cai, K., Venkatesh, P., Hung, A., Ng, M., Hall, C., Coventry, B., Lee, D. S., Chowhan, R., et al. (2025) · Molecular Cell

Metabolism, Diabetes, and CancerProtein Structure and Dynamics

Cited by 24

Tuning Insulin Receptor Signaling Using De Novo Designed Agonists

Wang, X., Cardoso, S., Cai, K., Venkatesh, P., Hung, A., Ng, M., Hall, C., Coventry, B., Lee, D., Chowhan, R., et al. (2024) · Molecular Cell

Metabolism, Diabetes, and CancerProtein Structure and Dynamics

Cited by 24

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

Kshirsagar, M., Meller, A., Humphreys, I. R., Sledzieski, S., Xu, Y., Dodhia, R., Horvitz, E., Berger, B., Bowman, G. R., Ferres, J. L., et al. (2025) · Nature Communications

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 23

Structurally Mapping Endogenous Heme in the CcmCDE Membrane Complex for Cytochrome c Biogenesis

Sutherland, M. C., Jarodsky, J. M., Ovchinnikov, S., Baker, D., & Kranz, R. G. (2018) · Journal of Molecular Biology

Metalloenzymes and iron-sulfur proteinsEnzyme Structure and Function

Cited by 23

Bond-centric modular design of protein assemblies

Wang, S., Favor, A., Kibler, R. D., Lubner, J. M., Borst, A. J., Coudray, N., Redler, R. L., Chiang, H. T., Sheffler, W., Hsia, Y., et al. (2025) · Nature Materials

Supramolecular Self-Assembly in MaterialsBiochemical and Structural Characterization

Cited by 22