David Baker

Research interests

Publications

• Generalized biomolecular modeling and design with RoseTTAFold All-Atom

  Science · 2024 · 10.1126/science.adl2528

• De novo design of protein structure and function with RFdiffusion

  Nature · 2023 · https://doi.org/10.1038/s41586-023-06415-8

• Robust deep learning–based protein sequence design using ProteinMPNN

  Science · 2022 · https://doi.org/10.1126/science.add2187

• Accurate prediction of protein structures and interactions using a three-track neural network

  Science · 2021 · https://doi.org/10.1126/science.abj8754

• Improved protein structure prediction using predicted interresidue orientations

  Proceedings of the National Academy of Sciences · 2020 · 10.1073/pnas.1914677117

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

  Science · 2020 · https://doi.org/10.1126/science.abd9909

• Macromolecular modeling and design in Rosetta: recent methods and frameworks

  Nature Methods · 2020 · 10.1038/s41592-020-0848-2

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

  Journal of Chemical Theory and Computation · 2017 · 10.1021/acs.jctc.7b00125

• The coming of age of de novo protein design

  Nature · 2016 · 10.1038/nature19946

• Plasma β-amyloid in Alzheimer’s disease and vascular disease

  Scientific Reports · 2016 · https://doi.org/10.1038/srep26801

• High-Resolution Comparative Modeling with RosettaCM

  Structure · 2013 · 10.1016/j.str.2013.08.005

• Rational HIV Immunogen Design to Target Specific Germline B Cell Receptors

  Science · 2013 · 10.1126/science.1234150

• Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction

  Science · 2010 · 10.1126/science.1190239

• Quantitative reactivity profiling predicts functional cysteines in proteomes

  Nature · 2010 · 10.1038/nature09472

• Rosetta3

  Methods in enzymology on CD-ROM/Methods in enzymology · 2010 · https://doi.org/10.1016/b978-0-12-381270-4.00019-6

• Predicting protein structures with a multiplayer online game

  Nature · 2010 · 10.1038/nature09304

• Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: Four approaches that performed well in CASP8

  Proteins Structure Function and Bioinformatics · 2009 · 10.1002/prot.22570

• Consistent blind protein structure generation from NMR chemical shift data

  Proceedings of the National Academy of Sciences · 2008 · 10.1073/pnas.0800256105

• De Novo Computational Design of Retro-Aldol Enzymes

  Science · 2008 · 10.1126/science.1152692

• Kemp elimination catalysts by computational enzyme design

  Nature · 2008 · 10.1038/nature06879

• Macromolecular Modeling with Rosetta

  Annual Review of Biochemistry · 2008 · 10.1146/annurev.biochem.77.062906.171838

• Toward High-Resolution de Novo Structure Prediction for Small Proteins

  Science · 2005 · 10.1126/science.1113801

• Protein structure prediction and analysis using the Robetta server

  Nucleic Acids Research · 2004 · https://doi.org/10.1093/nar/gkh468

• Protein Structure Prediction Using Rosetta

  Methods in enzymology on CD-ROM/Methods in enzymology · 2004 · 10.1016/s0076-6879(04)83004-0

• Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations

  Journal of Molecular Biology · 2003 · 10.1016/s0022-2836(03)00670-3

• Design of a Novel Globular Protein Fold with Atomic-Level Accuracy

  Science · 2003 · 10.1126/science.1089427

• Protein Structure Prediction and Structural Genomics

  Science · 2001 · 10.1126/science.1065659

• Contact order, transition state placement and the refolding rates of single domain proteins 1 1Edited by P. E. Wright

  Journal of Molecular Biology · 1998 · 10.1006/jmbi.1998.1645

• Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions

  Journal of Molecular Biology · 1997 · 10.1006/jmbi.1997.0959

Current projects

No projects listed.