Detection of Protein Coding Sequences Using a Mixture Model for Local Protein Amino Acid Sequence. - Edward C. Thayer; Chris Bystroff; David Baker 001 (J. Comput. Biol., 2000)

Protein Structure Prediction Using Rosetta. - Carol A. Rohl; Charlie E. M. Strauss; Kira M. S. Misura; David Baker 001 (Numerical Computer Methods, Part D, 2004)

Protein structure prediction and analysis using the Robetta server. - David E. Kim; Dylan Chivian; David Baker 001 (Nucleic Acids Res., 2004)

Parallelization and performance characterization of protein 3D structure prediction of Rosetta. - Wenlong Li 003; Tao Wang 003; Eric Q. Li; David Baker 001; Li Jin; Steven Ge; Yurong Chen 001; Yimin Zhang 002 (IPDPS, 2006)

Poster reception - High resolution, high throughput protein structure prediction using IBM Blue Gene supercomputers: predicting CASP targets in record time. - Ross C. Walker; Srivatsan Raman; David Baker 001 (SC, 2006)

Feature Selection Methods for Improving Protein Structure Prediction with Rosetta. - Ben Blum; Michael I. Jordan; David E. Kim; Rhiju Das; Philip Bradley; David Baker 001 (NIPS, 2007)

Advances in Rosetta protein structure prediction on massively parallel systems. - Srivatsan Raman; Bin Qian; David Baker 001; Ross C. Walker (IBM J. Res. Dev., 2008)

Structure similarity measure with penalty for close non-equivalent residues. - Ruslan Sadreyev; Shuoyong Shi; David Baker 001; Nick V. Grishin (Bioinform., 2009)

Computation of Conformational Coupling in Allosteric Proteins. - Brian A. Kidd; David Baker 001; Wendy E. Thomas (PLoS Comput. Biol., 2009)

The challenge of designing scientific discovery games. - Seth Cooper; Adrien Treuille; Janos Barbero; Andrew Leaver-Fay; Kathleen Tuite; Firas Khatib; Alex Cho Snyder; Michael Beenen; David Salesin; David Baker 001; Zoran Popovic (FDG, 2010)

Predicting protein structures with a multiplayer online game. - Seth Cooper; Firas Khatib; Adrien Treuille; Janos Barbero; Jeehyung Lee; Michael Beenen; Andrew Leaver-Fay; David Baker 001; Zoran Popovic; Foldit players (Nat., 2010)

Analysis of social gameplay macros in the Foldit cookbook. - Seth Cooper; Firas Khatib; Ilya Makedon; Hao Lü; Janos Barbero; David Baker 001; James Fogarty; Zoran Popovic; Foldit players (FDG, 2011)

Algorithm discovery by protein folding game players. - Firas Khatib; Seth Cooper; Michael D. Tyka; Kefan Xu; Ilya Makedon; Zoran Popovic; David Baker 001; Foldit players (Proc. Natl. Acad. Sci. USA, 2011)

Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers. - Michael D. Tyka; Kenneth Jung; David Baker 001 (J. Comput. Chem., 2012)

Computational design of ligand-binding proteins with high affinity and selectivity. - Christine E. Tinberg; Sagar D. Khare; Jiayi Dou; Lindsey Doyle; Jorgen W. Nelson; Alberto Schena; Wojciech Jankowski; Charalampos G. Kalodimos; Kai Johnsson; Barry L. Stoddard; David Baker 001 (Nat., 2013)

Proof of principle for epitope-focused vaccine design. - Bruno E. Correia; John T. Bates; Rebecca J. Loomis; Gretchen Baneyx; Chris Carrico; Joseph G. Jardine; Peter Rupert; Colin E. Correnti; Oleksandr Kalyuzhniy; Vinayak Vittal; Mary J. Connell; Eric Stevens; et al. (Nat., 2014)

Accurate design of co-assembling multi-component protein nanomaterials. - Neil P. King; Jacob B. Bale; William Sheffler; Dan E. McNamara; Shane Gonen; Tamir Gonen; Todd O. Yeates; David Baker 001 (Nat., 2014)

High-Resolution Modeling of Transmembrane Helical Protein Structures from Distant Homologues. - Kuang-Yui M. Chen; Jiaming Sun; Jason S. Salvo; David Baker 001; Patrick Barth (PLoS Comput. Biol., 2014)

Removing T-cell epitopes with computational protein design. - Chris King; Esteban N. Garza; Ronit Mazor; Jonathan L. Linehan; Ira Pastan; Marion Pepper; David Baker 001 (Proc. Natl. Acad. Sci. USA, 2014)

Constructing Structural Profiles for Protein Torsion Angle Prediction. - Zafer Aydin; David Baker 001; William Stafford Noble (BIOINFORMATICS, 2015)

Template Scoring Methods for Protein Torsion Angle Prediction. - Zafer Aydin; David Baker 001; William Stafford Noble (BIOSTEC (Selected Papers), 2015)

Exploring the repeat protein universe through computational protein design. - T. J. Brunette; Fabio Parmeggiani; Po-Ssu Huang; Gira Bhabha; Damian C. Ekiert; Susan E. Tsutakawa; Greg L. Hura; John A. Tainer; David Baker 001 (Nat., 2015)

Rational design of α-helical tandem repeat proteins with closed architectures. - Lindsey Doyle; Jazmine Hallinan; Jill Bolduc; Fabio Parmeggiani; David Baker 001; Barry L. Stoddard; Philip Bradley (Nat., 2015)

FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants. - David Bednar; Koen Beerens; Eva Sebestova; Jaroslav Bendl; Sagar D. Khare; Radka Chaloupkova; Zbynek Prokop; Jan Brezovsky; David Baker 001; Jirí Damborský (PLoS Comput. Biol., 2015)

CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge. - Richard D. Smith; Kelly L. Damm-Ganamet; James B. Dunbar Jr.; Aqeel Ahmed; Krishnapriya Chinnaswamy; James Delproposto; Ginger Kubish; Christine E. Tinberg; Sagar D. Khare; Jiayi Dou; Lindsey Doyle; Jeanne A. Stuckey; et al. (J. Chem. Inf. Model., 2016)

Accurate de novo design of hyperstable constrained peptides. - Gaurav Bhardwaj; Vikram Khipple Mulligan; Christopher D. Bahl; Jason M. Gilmore; Peta J. Harvey; Olivier Cheneval; Garry W. Buchko; Surya V. S. R. K. Pulavarti; Quentin Kaas; Alexander Eletsky; Po-Ssu Huang; William A. Johnsen; et al. (Nat., 2016)

Design of a hyperstable 60-subunit protein icosahedron. - Yang Hsia; Jacob B. Bale; Shane Gonen; Dan Shi; William Sheffler; Kimberly K. Fong; Una Nattermann; Chunfu Xu; Po-Ssu Huang; Rashmi Ravichandran; Sue Yi; Trisha N. Davis; et al. (Nat., 2016)

Corrigendum: Design of a hyperstable 60-subunit protein icosahedron. - Yang Hsia; Jacob B. Bale; Shane Gonen; Dan Shi; William Sheffler; Kimberly K. Fong; Una Nattermann; Chunfu Xu; Po-Ssu Huang; Rashmi Ravichandran; Sue Yi; Trisha N. Davis; et al. (Nat., 2016)

Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta. - Robert Kleffner; Jeff Flatten; Andrew Leaver-Fay; David Baker 001; Justin B. Siegel; Firas Khatib; Seth Cooper (Bioinform., 2017)

Massively parallel de novo protein design for targeted therapeutics. - Aaron Chevalier; Daniel-Adriano Silva; Gabriel J. Rocklin; Derrick R. Hicks; Renan Vergara; Patience Murapa; Steffen M. Bernard; Lu Zhang; Kwok-Ho Lam; Guorui Yao; Christopher D. Bahl; Shin-Ichiro Miyashita; et al. (Nat., 2017)

Surrogate Wnt agonists that phenocopy canonical Wnt and β-catenin signalling. - Claudia Y. Janda; Luke T. Dang; Changjiang You; Junlei Chang; Wim de Lau; Zhendong A. Zhong; Kelley S. Yan; Owen Marecic; Dirk Siepe; Xingnan Li; James D. Moody; Bart O. Williams; et al. (Nat., 2017)

Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3. - Stefan Schoebel; Wei Mi; Alexander Stein; Sergey Ovchinnikov 001; Ryan E. Pavlovicz; Frank DiMaio; David Baker 001; Melissa G. Chambers; Huayou Su; Dongsheng Li; Tom A. Rapoport; Maofu Liao (Nat., 2017)

De novo design of a fluorescence-activating β-barrel. - Jiayi Dou; Anastassia A. Vorobieva; William Sheffler; Lindsey Doyle; Hahnbeom Park; Matthew J. Bick; Binchen Mao; Glenna W. Foight; Min-Yen Lee; Lauren A. Gagnon; Lauren P. Carter; Banumathi Sankaran; et al. (Nat., 2018)

Programmable design of orthogonal protein heterodimers. - Zibo Chen; Scott E. Boyken; Mengxuan Jia; Florian Busch; David Flores-Solis; Matthew J. Bick; Peilong Lu; Zachary L. VanAernum; Aniruddha Sahasrabuddhe; Robert A. Langan; Sherry Bermeo; T. J. Brunette; et al. (Nat., 2019)

De novo protein design by citizen scientists. - Brian Koepnick; Jeff Flatten; Tamir Husain; Alex Ford; Daniel-Adriano Silva; Matthew J. Bick; Aaron Bauer 002; Gaohua Liu; Yojiro Ishida; Alexander Boykov; Roger D. Estep; Susan Kleinfelter; et al. (Nat., 2019)

De novo design of bioactive protein switches. - Robert A. Langan; Scott E. Boyken; Andrew H. Ng; Jennifer A. Samson; Galen Dods; Alexandra M. Westbrook; Taylor H. Nguyen; Marc J. Lajoie; Zibo Chen; Stephanie Berger; Vikram Khipple Mulligan; John E. Dueber; et al. (Nat., 2019)

Modular and tunable biological feedback control using a de novo protein switch. - Andrew H. Ng; Taylor H. Nguyen; Mariana Gómez-Schiavon; Galen Dods; Robert A. Langan; Scott E. Boyken; Jennifer A. Samson; Lucas M. Waldburger; John E. Dueber; David Baker 001; Hana El-Samad (Nat., 2019)

De novo design of potent and selective mimics of IL-2 and IL-15. - Daniel-Adriano Silva; Shawn Yu; Umut Y. Ulge; Jamie B. Spangler; Kevin M. Jude; Carlos Labão-Almeida; Lestat R. Ali; Alfredo Quijano-Rubio; Mikel Ruterbusch; Isabel Leung; Tamara Biary; Stephanie J. Crowley; et al. (Nat., 2019)

Protein contact prediction using metagenome sequence data and residual neural networks. - Qi Wu 016; Zhenling Peng; Ivan Anishchenko; Qian Cong; David Baker 001; Jianyi Yang 002 (Bioinform., 2020)

Better together: Elements of successful scientific software development in a distributed collaborative community. - Julia Koehler Leman; Brian D. Weitzner; P. Douglas Renfrew; Steven M. Lewis; Rocco Moretti; Andrew M. Watkins; Vikram Khipple Mulligan; Sergey Lyskov; Jared Adolf-Bryfogle; Jason W. Labonte; Justyna Krys; RosettaCommons Consortium; et al. (PLoS Comput. Biol., 2020)

Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds. - Brian Coventry; David Baker 001 (PLoS Comput. Biol., 2021)

Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs. - Neeladri Sen; Ivan Anishchenko; Nicola Bordin; Ian Sillitoe; Sameer Velankar; David Baker 001; Christine A. Orengo (Briefings Bioinform., 2022)

Interpreting neural networks for biological sequences by learning stochastic masks. - Johannes Linder; Alyssa La Fleur; Zibo Chen; Ajasja Ljubetic; David Baker 001; Sreeram Kannan; Georg Seelig (Nat. Mach. Intell., 2022)

Diffusion Probabilistic Modeling of Protein Backbones in 3D for the motif-scaffolding problem. - Brian L. Trippe; Jason Yim; Doug Tischer; David Baker 001; Tamara Broderick; Regina Barzilay; Tommi S. Jaakkola (ICLR, 2023)

Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock. - William Sheffler; Erin C. Yang; Quinton Dowling; Yang Hsia; Chelsea N. Fries; Jenna Stanislaw; Mark D. Langowski; Marisa Brandys; Zhe Li; Rebecca Skotheim; Andrew J. Borst; Alena Khmelinskaia; et al. (PLoS Comput. Biol., 2023)