David A. Baker

Research Statement

AI generated · 12h ago

David A. Baker's indexed work centers on computational protein structure prediction and de novo design, spanning fragment-assembly methods, energy-function development, and modern deep learning. His senior-authored RFdiffusion for de novo design of protein structure and function and ProteinMPNN for robust deep learning–based protein sequence design are among the most-cited in the field, while earlier work on the Robetta server for automated structure prediction and analysis established widely used infrastructure. Foundational contributions include contact order as a determinant of protein refolding rates and atomic-accuracy design of a novel globular protein fold. Beyond these, his middle-author contributions include Rosetta3, a modular macromolecular modeling and design suite, and the Rosetta all-atom energy function for macromolecular modeling and design, both central to the software ecosystem underlying his prediction and design work. No software tools, datasets, grants, or patents are separately indexed beyond these publications. Read together, the works trace a line from fragment-based structure assembly and energy-function refinement to deep-learning generative design, with collaborators such as Daniel Wrapp reflecting the broader structural-biology context in which this toolkit is applied.

Most Cited Works

De novo design of protein structure and function with RFdiffusion

Joseph L Watson, David Juergens, Nathaniel R Bennett, Brian L Trippe, Jason Yim, Helen E Eisenach, Woody Ahern, Andrew J Borst, Robert J Ragotte, Lukas F Milles, Basile I M Wicky, Nikita Hanikel, Samuel J Pellock, Alexis Courbet, William Sheffler, Jue Wang, Preetham Venkatesh, Isaac Sappington, Susana Vázquez Torres, Anna Lauko, Valentin De Bortoli, Emile Mathieu, Sergey Ovchinnikov, Regina Barzilay, Tommi S Jaakkola, Frank DiMaio, Minkyung Baek, David Baker

Nature2023

Research Areas

Protein Structure and DynamicsEnzyme Structure and FunctionBiochemical and Structural CharacterizatRNA and protein synthesis mechanismsChemical Synthesis and Analysis

Affiliations & Education

Education

1988–2009
University of California, Berkeley(US)
PhD · Biochemistry
2005–2021
Harvard University(US)
B.A. · Biology

Employment

2003–present· now
University of Washington(US)
Professor · Biochemistry

Loading ORCID activity...

Sources

Research Statement

Most Cited Works

De novo design of protein structure and function with RFdiffusion

Research Areas

Affiliations & Education

Education

Employment

Robust deep learning–based protein sequence design using ProteinMPNN

Protein structure prediction and analysis using the Robetta server

Quantitative reactivity profiling predicts functional cysteines in proteomes

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