Baker, David

Computational design of serine hydrolases

Lauko, A., Pellock, S. J., Sumida, K. H., Anishchenko, I., Juergens, D., Ahern, W., Jeung, J., Shida, A. F., Hunt, A., Kalvet, I., et al. (2025) · Science

Protein Structure and DynamicsEnzyme Catalysis and Immobilization

Cited by 235

Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold

Azoitei, M. L., Correia, B. E., Ban, Y.-E. A., Carrico, C., Kalyuzhniy, O., Chen, L., Schroeter, A., Huang, P.-S., McLellan, J. S., Kwong, P. D., et al. (2011) · Science

Protein Structure and DynamicsBiochemical and Structural Characterization

Cited by 224

Large-scale determination of previously unsolved protein structures using evolutionary information

Ovchinnikov, S., Kinch, L., Park, H., Liao, Y., Pei, J., Kim, D. E., Kamisetty, H., Grishin, N. V., & Baker, D. (2015) · eLife

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 222

The Acidic Transcription Activator Gcn4 Binds the Mediator Subunit Gal11/Med15 Using a Simple Protein Interface Forming a Fuzzy Complex

Brzovic, P. S., Heikaus, C. C., Kisselev, L., Vernon, R., Herbig, E., Pacheco, D., Warfield, L., Littlefield, P., Baker, D., Klevit, R. E., et al. (2011) · Molecular Cell

Protein Structure and DynamicsGenomics and Chromatin Dynamics

Cited by 203

A Novel Semi-biosynthetic Route for Artemisinin Production Using Engineered Substrate-Promiscuous P450 BM3

Dietrich, J. A., Yoshikuni, Y., Fisher, K. J., Woolard, F. X., Ockey, D., McPhee, D. J., Renninger, N. S., Chang, M. C. Y., Baker, D., & Keasling, J. D. (2009) · ACS Chemical Biology

Enzyme Catalysis and ImmobilizationMicrobial Metabolic Engineering and Bioproduction

Cited by 186

Origins of coevolution between residues distant in protein 3D structures

Anishchenko, I., Ovchinnikov, S., Kamisetty, H., & Baker, D. (2017) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 185

Language models generalize beyond natural proteins

Verkuil, R., Kabeli, O., Du, Y., Wicky, B. I. M., Milles, L. F., Dauparas, J., Baker, D., Ovchinnikov, S., Sercu, T., & Rives, A. (2022) · bioRxiv (Cold Spring Harbor Laboratory)

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 181

Rapid online buffer exchange for screening of proteins, protein complexes and cell lysates by native mass spectrometry

VanAernum, Z. L., Busch, F., Jones, B. J., Jia, M., Chen, Z., Boyken, S. E., Sahasrabuddhe, A., Baker, D., & Wysocki, V. H. (2020) · Nature Protocols

Mass Spectrometry Techniques and ApplicationsAdvanced Proteomics Techniques and Applications

Cited by 169

What has de novo protein design taught us about protein folding and biophysics?

Baker, D. (2019) · Protein Science

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 161

An improved protein decoy set for testing energy functions for protein structure prediction

Tsai, J., Bonneau, R., Morozov, A. V., Kuhlman, B., Rohl, C. A., & Baker, D. (2003) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 158

Next-Generation Surrogate Wnts Support Organoid Growth and Deconvolute Frizzled Pleiotropy In Vivo

Miao, Y., Ha, A., de Lau, W., Yuki, K., Santos, A. J. M., You, C., Geurts, M. H., Puschhof, J., Pleguezuelos-Manzano, C., Peng, W. C., et al. (2020) · Cell Stem Cell

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

Cited by 151

Protein sequence design by conformational landscape optimization

Norn, C., Wicky, B. I. M., Juergens, D., Liu, S., Kim, D., Tischer, D., Koepnick, B., Anishchenko, I., Players, F., Baker, D., et al. (2021) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 144

A Computationally Designed Inhibitor of an Epstein-Barr Viral Bcl-2 Protein Induces Apoptosis in Infected Cells

Procko, E., Berguig, G. Y., Shen, B. W., Song, Y., Frayo, S., Convertine, A. J., Margineantu, D., Booth, G., Correia, B. E., Cheng, Y., et al. (2014) · Cell

Cell death mechanisms and regulationChemical Synthesis and Analysis

Cited by 127

Peptide-binding specificity prediction using fine-tuned protein structure prediction networks

Motmaen, A., Dauparas, J., Baek, M., Abedi, M. H., Baker, D., & Bradley, P. (2023) · Proceedings of the National Academy of Sciences

vaccines and immunoinformatics approachesProtein Structure and Dynamics

Cited by 124

Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site

Strauch, E.-M., Bernard, S. M., La, D., Bohn, A. J., Lee, P. S., Anderson, C. E., Nieusma, T., Holstein, C. A., Garcia, N. K., Hooper, K. A., et al. (2017) · Nature Biotechnology

Influenza Virus Research StudiesProtein Structure and Dynamics

Cited by 119

Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle

Wang, Y., Gallagher, L. A., Andrade, P. A., Liu, A., Humphreys, I. R., Turkarslan, S., Cutler, K. J., Arrieta-Ortiz, M. L., Li, Y., Radey, M. C., et al. (2023) · Cell

Bacterial Genetics and BiotechnologyMicrobial Community Ecology and Physiology

Cited by 108

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. (2023) · bioRxiv (Cold Spring Harbor Laboratory)

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 106

Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem

Trippe, B. L., Yim, J., Tischer, D., Baker, D., Broderick, T., Barzilay, R., & Jaakkola, T. (2022) · arXiv

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 92

Design of stimulus-responsive two-state hinge proteins

Praetorius, F., Leung, P. J. Y., Tessmer, M. H., Broerman, A., Demakis, C., Dishman, A. F., Pillai, A., Idris, A., Juergens, D., Dauparas, J., et al. (2023) · Science

Protein Structure and DynamicsBiochemical and Structural Characterization

Cited by 90

Design of stimulus-responsive two-state hinge proteins

Praetorius, F., Leung, P. J. Y., Tessmer, M. H., Broerman, A., Demakis, C., Dishman, A. F., Pillai, A., Idris, A., Juergens, D., Dauparas, J., et al. (2023) · Science

Protein Structure and DynamicsBiochemical and Structural Characterization

Cited by 90

Predicting protein-protein interactions in the human proteome

Zhang, J., Humphreys, I. R., Pei, J., Kim, J., Choi, C., Yuan, R., Durham, J., Liu, S., Choi, H.-J., Baek, M., et al. (2025) · Science

Bioinformatics and Genomic NetworksProtein Structure and Dynamics

Cited by 87

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

Determining crystal structures through crowdsourcing and coursework

Horowitz, S., Koepnick, B., Martin, R., Tymieniecki, A., Winburn, A. A., Cooper, S., Flatten, J., Rogawski, D. S., Koropatkin, N. M., Hailu, T. T., et al. (2016) · Nature Communications

Enzyme Structure and FunctionProtein Structure and Dynamics

Cited by 75

Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease

Case, J. B., Chen, R. E., Cao, L., Ying, B., Winkler, E. S., Johnson, M., Goreshnik, I., Pham, M. N., Shrihari, S., Kafai, N. M., et al. (2021) · Cell Host & Microbe

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

Cited by 73