Baker, David

Computed structures of core eukaryotic protein complexes

Humphreys, I. R., Pei, J., Baek, M., Krishnakumar, A., Anishchenko, I., Ovchinnikov, S., Zhang, J., Ness, T. J., Banjade, S., Bagde, S. R., et al. (2021) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 542

Structures of core eukaryotic protein complexes

Humphreys, I. R., Pei, J., Baek, M., Krishnakumar, A., Anishchenko, I., Ovchinnikov, S., Zhang, J., Ness, T. J., Banjade, S., Bagde, S., et al. (2021) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 541

Crystal structure of a monomeric retroviral protease solved by protein folding game players

Foldit Contenders Group, Khatib, F., Foldit Void Crushers Group, DiMaio, F., Cooper, S., Kazmierczyk, M., Gilski, M., Krzywda, S., Zabranska, H., Pichova, I., et al. (2011) · Nature Structural & Molecular Biology

Enzyme Structure and FunctionProtein Structure and Dynamics

Cited by 540

De novo design of potent and selective mimics of IL-2 and IL-15

Silva, D.-A., Yu, S., Ulge, U. Y., Spangler, J. B., Jude, K. M., Labão-Almeida, C., Ali, L. R., Quijano-Rubio, A., Ruterbusch, M., Leung, I., et al. (2019) · Nature

Protein Structure and DynamicsChemical Synthesis and Analysis

Cited by 531

Protein structure determination using metagenome sequence data

Ovchinnikov, S., Park, H., Varghese, N., Huang, P.-S., Pavlopoulos, G. A., Kim, D. E., Kamisetty, H., Kyrpides, N. C., & Baker, D. (2017) · Science

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 520

High-resolution mapping of protein sequence-function relationships

Fowler, D. M., Araya, C. L., Fleishman, S. J., Kellogg, E. H., Stephany, J. J., Baker, D., & Fields, S. (2010) · Nature Methods

Chemical Synthesis and AnalysisProtein Structure and Dynamics

Cited by 516

Global analysis of protein folding using massively parallel design, synthesis, and testing

Rocklin, G. J., Chidyausiku, T. M., Goreshnik, I., Ford, A., Houliston, S., Lemak, A., Carter, L., Ravichandran, R., Mulligan, V. K., Chevalier, A., et al. (2017) · Science

Protein Structure and DynamicsChemical Synthesis and Analysis

Cited by 501

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

Massively parallel de novo protein design for targeted therapeutics

Chevalier, A., Silva, D.-A., Rocklin, G. J., Hicks, D. R., Vergara, R., Murapa, P., Bernard, S. M., Zhang, L., Lam, K.-H., Yao, G., et al. (2017) · Nature

Protein Structure and DynamicsMonoclonal and Polyclonal Antibodies Research

Cited by 453

Surrogate Wnt agonists that phenocopy canonical Wnt and β-catenin signalling

Janda, C. Y., Dang, L. T., You, C., Chang, J., de Lau, W., Zhong, Z. A., Yan, K. S., Marecic, O., Siepe, D., Li, X., et al. (2017) · Nature

Wnt/β-catenin signaling in development and cancerHedgehog Signaling Pathway Studies

Cited by 403

Improving de novo protein binder design with deep learning

Bennett, N. R., Coventry, B., Goreshnik, I., Huang, B., Allen, A., Vafeados, D., Peng, Y. P., Dauparas, J., Baek, M., Stewart, L., et al. (2023) · Nature Communications

Protein Structure and Dynamicsvaccines and immunoinformatics approaches

Cited by 402

Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA

Baek, M., McHugh, R., Anishchenko, I., Jiang, H., Baker, D., & DiMaio, F. (2024) · Nature Methods

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 372

De novo design of a fluorescence-activating β-barrel

Dou, J., Vorobieva, A. A., Sheffler, W., Doyle, L. A., Park, H., Bick, M. J., Mao, B., Foight, G. W., Lee, M. Y., Gagnon, L. A., et al. (2018) · Nature

Protein Structure and DynamicsBiochemical and Structural Characterization

Cited by 351

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

Engineering an allosteric transcription factor to respond to new ligands

Taylor, N. D., Garruss, A. S., Moretti, R., Chan, S., Arbing, M. A., Cascio, D., Rogers, J. K., Isaacs, F. J., Kosuri, S., Baker, D., et al. (2016) · Nature Methods

Gene Regulatory Network AnalysisMicrobial Metabolic Engineering and Bioproduction

Cited by 328

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

Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta

DiMaio, F., Tyka, M. D., Baker, M. L., Chiu, W., & Baker, D. (2009) · Journal of Molecular Biology

Advanced Electron Microscopy Techniques and ApplicationsProtein Structure and Dynamics

Cited by 295

Progress in Modeling of Protein Structures and Interactions.

Schueler-Furman, O., Wang, C., Bradley, P., Misura, K., & Baker, D. (2005) · Science

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 294

Elicitation of structure-specific antibodies by epitope scaffolds

Ofek, G., Guenaga, F. J., Schief, W. R., Skinner, J., Baker, D., Wyatt, R., & Kwong, P. D. (2010) · Proceedings of the National Academy of Sciences

HIV Research and Treatmentvaccines and immunoinformatics approaches

Cited by 278

High thermodynamic stability of parametrically designed helical bundles

Huang, P.-S., Oberdorfer, G., Xu, C., Pei, X. Y., Nannenga, B. L., Rogers, J. M., DiMaio, F., Gonen, T., Luisi, B., & Baker, D. (2014) · Science

Protein Structure and DynamicsChemical Synthesis and Analysis

Cited by 277

De novo design of modular and tunable protein biosensors

Quijano-Rubio, A., Yeh, H.-W., Park, J., Lee, H., Langan, R. A., Boyken, S. E., Lajoie, M. J., Cao, L., Chow, C. M., Miranda, M. C., et al. (2021) · Nature

Protein Structure and DynamicsBiochemical and Structural Characterization

Cited by 260

Improved protein structure refinement guided by deep learning based accuracy estimation

Hiranuma, N., Park, H., Baek, M., Anishchenko, I., Dauparas, J., & Baker, D. (2021) · Nature Communications

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 243

Protein interaction networks revealed by proteome coevolution

Cong, Q., Anishchenko, I., Ovchinnikov, S., & Baker, D. (2019) · Science

Bioinformatics and Genomic NetworksProtein Structure and Dynamics

Cited by 241