Baker, David

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

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

Quantitative reactivity profiling predicts functional cysteines in proteomes

Weerapana, E., Wang, C., Simon, G. M., Richter, F., Khare, S., Dillon, M. B. D., Bachovchin, D. A., Mowen, K., Baker, D., & Cravatt, B. F. (2010) · Nature

Redox biology and oxidative stressAdvanced Proteomics Techniques and Applications

Cited by 1,684

Protein Structure Prediction and Structural Genomics

Baker, D., & Sali, A. (2001) · Science

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 1,587

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

Alford, R. F., Leaver-Fay, A., Jeliazkov, J. R., O’Meara, M. J., DiMaio, F. P., Park, H., Shapovalov, M. V., Renfrew, P. D., Mulligan, V. K., Kappel, K., et al. (2017) · Journal of Chemical Theory and Computation

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 1,532

The coming of age of de novo protein design

Huang, P.-S., Boyken, S. E., & Baker, D. (2016) · Nature

Protein Structure and DynamicsChemical Synthesis and Analysis

Cited by 1,478

Improved protein structure prediction using predicted interresidue orientations

Yang, J., Anishchenko, I., Park, H., Peng, Z., Ovchinnikov, S., & Baker, D. (2020) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 1,421

Predicting protein structures with a multiplayer online game

Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., Leaver-Fay, A., Baker, D., Popović, Z., & players, F. (2010) · Nature

Protein Structure and DynamicsDigital Games and Media

Cited by 1,368

Generalized biomolecular modeling and design with RoseTTAFold All-Atom

Krishna, R., Wang, J., Ahern, W., Sturmfels, P., Venkatesh, P., Kalvet, I., Lee, G. R., Morey-Burrows, F. S., Anishchenko, I., Humphreys, I. R., et al. (2024) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 978

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Leman, J. K., Weitzner, B. D., Lewis, S. M., Adolf-Bryfogle, J., Alam, N., Alford, R. F., Aprahamian, M., Baker, D., Barlow, K. A., Barth, P., et al. (2020) · Nature Methods

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 888

Consistent blind protein structure generation from NMR chemical shift data

Shen, Y., Lange, O., Delaglio, F., Rossi, P., Aramini, J. M., Liu, G., Eletsky, A., Wu, Y., Singarapu, K. K., Lemak, A., et al. (2008) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsAdvanced NMR Techniques and Applications

Cited by 855

Rational HIV Immunogen Design to Target Specific Germline B Cell Receptors

Jardine, J., Julien, J.-P., Menis, S., Ota, T., Kalyuzhniy, O., McGuire, A., Sok, D., Huang, P.-S., MacPherson, S., Jones, M., et al. (2013) · Science

HIV Research and TreatmentSARS-CoV-2 and COVID-19 Research

Cited by 770

De novo design of picomolar SARS-CoV-2 miniprotein inhibitors

Cao, L., Goreshnik, I., Coventry, B., Case, J. B., Miller, L., Kozodoy, L., Chen, R. E., Carter, L., Walls, A. C., Park, Y.-J., et al. (2020) · Science

SARS-CoV-2 and COVID-19 Researchvaccines and immunoinformatics approaches

Cited by 742

An engineered microbial platform for direct biofuel production from brown macroalgae

Wargacki, A. J., Leonard, E., Win, M. N., Regitsky, D. D., Santos, C. N. S., Kim, P. B., Cooper, S. R., Raisner, R. M., Herman, A., Sivitz, A. B., et al. (2012) · Science

Microbial Metabolic Engineering and BioproductionBiofuel production and bioconversion

Cited by 734

High-Resolution Microtubule Structures Reveal the Structural Transitions in αβ-Tubulin upon GTP Hydrolysis

Alushin, G. M., Lander, G. C., Kellogg, E. H., Zhang, R., Baker, D., & Nogales, E. (2014) · Cell

Microtubule and mitosis dynamicsCancer Treatment and Pharmacology

Cited by 696

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

Ovchinnikov, S., Kamisetty, H., & Baker, D. (2014) · eLife

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 629

De novo protein design by deep network hallucination

Anishchenko, I., Chidyausiku, T. M., Ovchinnikov, S., Pellock, S. J., & Baker, D. (2020) · Nature

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 629

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

Fleishman, S. J., Whitehead, T. A., Ekiert, D. C., Dreyfus, C., Corn, J. E., Strauch, E.-M., Wilson, I. A., & Baker, D. (2011) · Science

Protein Structure and DynamicsInfluenza Virus Research Studies

Cited by 585

Design of protein-binding proteins from the target structure alone

Cao, L., Coventry, B., Goreshnik, I., Huang, B., Sheffler, W., Park, J. S., Jude, K. M., Marković, I., Kadam, R. U., Verschueren, K. H. G., et al. (2022) · Nature

Protein Structure and DynamicsChemical Synthesis and Analysis

Cited by 577

Principles for designing ideal protein structures

Koga, N., Tatsumi-Koga, R., Liu, G., Xiao, R., Acton, T. B., Montelione, G. T., & Baker, D. (2012) · Nature

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 564

Proof of principle for epitope-focused vaccine design

Correia, B. E., Bates, J. T., Loomis, R. J., Baneyx, G., Carrico, C., Jardine, J. G., Rupert, P., Correnti, C., Kalyuzhniy, O., Vittal, V., et al. (2014) · Nature

vaccines and immunoinformatics approachesSARS-CoV-2 and COVID-19 Research

Cited by 555