David Baker

According to our database, David Baker authored at least 45 papers between 2000 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

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, Neil P. King, David Baker

PLoS Comput. Biol., 2023

Diffusion Probabilistic Modeling of Protein Backbones in 3D for the motif-scaffolding problem.

Brian L. Trippe, Jason Yim, Doug Tischer, David Baker, Tamara Broderick, Regina Barzilay, Tommi S. Jaakkola

Proceedings of the Eleventh International Conference on Learning Representations, 2023

2022

Interpreting neural networks for biological sequences by learning stochastic masks.

Johannes Linder, Alyssa La Fleur, Zibo Chen, Ajasja Ljubetic, David Baker, Sreeram Kannan, Georg Seelig

Nat. Mach. Intell., 2022

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, Christine A. Orengo

Briefings Bioinform., 2022

2021

Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds.

Brian Coventry, David Baker

PLoS Comput. Biol., 2021

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, Christopher Bystroff, William R. Schief, Dominik Gront, Ora Schueler-Furman, David Baker, Philip Bradley, Roland L. Dunbrack Jr., Tanja Kortemme, Andrew Leaver-Fay, Charlie E. M. Strauss, Jens Meiler, Brian Kuhlman, Jeffrey J. Gray, Richard Bonneau

PLoS Comput. Biol., 2020

Protein contact prediction using metagenome sequence data and residual neural networks.

Qi Wu, Zhenling Peng, Ivan Anishchenko, Qian Cong, David Baker, Jianyi Yang

Bioinform., 2020

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, Enrique Marcos, Carl D. Walkey, Brian D. Weitzner, Fátima Pardo Avila, Javier Castellanos, Lauren P. Carter, Lance J. Stewart, Stanley R. Riddell, Marion Pepper, Gonçalo J. L. Bernardes, Michael Dougan, K. Christopher Garcia, David Baker

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, Hana El-Samad

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, Walter R. P. Novak, Hana El-Samad, David Baker

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, Gaohua Liu, Yojiro Ishida, Alexander Boykov, Roger D. Estep, Susan Kleinfelter, Toke Nørgård-Solano, Linda Wei, Foldit players, Gaetano T. Montelione, Frank DiMaio, Zoran Popovic, Firas Khatib, Seth Cooper, David Baker

Nat., 2019

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, Vikram Khipple Mulligan, Lauren P. Carter, Frank DiMaio, Nikolaos G. Sgourakis, Vicki H. Wysocki, David Baker

Nat., 2019

2018

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, Sergey Ovchinnikov, Enrique Marcos, Po-Ssu Huang, Joshua C. Vaughan, Barry L. Stoddard, David Baker

Nat., 2018

2017

Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3.

Stefan Schoebel, Wei Mi, Alexander Stein, Sergey Ovchinnikov, Ryan E. Pavlovicz, Frank DiMaio, David Baker, Melissa G. Chambers, Huayou Su, Dongsheng Li, Tom A. Rapoport, Maofu Liao

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, Hans Clevers, Jacob Piehler, David Baker, Calvin J. Kuo, K. Christopher Garcia

Nat., 2017

Massively parallel <i>de novo</i> 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, Inna Goreshnik, James T. Fuller, Merika T. Koday, Cody M. Jenkins, Tom Colvin, Lauren P. Carter, Alan Bohn, Cassie M. Bryan, D. Alejandro Fernández-Velasco, Lance J. Stewart, Min Dong, Xuhui Huang, Rongsheng Jin, Ian A. Wilson, Deborah H. Fuller, David Baker

Nat., 2017

Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta.

Robert Kleffner, Jeff Flatten, Andrew Leaver-Fay, David Baker, Justin B. Siegel, Firas Khatib, Seth Cooper

Bioinform., 2017

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, Tamir Gonen, Neil P. King, David Baker

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, Tamir Gonen, Neil P. King, David Baker

Nat., 2016

Accurate <i>de novo</i> 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, Per Greisen, Gabriel J. Rocklin, Yifan Song, Thomas W. Linsky, Andrew M. Watkins, Stephen A. Rettie, Xianzhong Xu, Lauren P. Carter, Richard Bonneau, James M. Olson, Evangelos A. Coutsias, Colin E. Correnti, Thomas Szyperski, David J. Craik, David Baker

Nat., 2016

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, David Baker, Heather A. Carlson

J. Chem. Inf. Model., 2016

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, Jirí Damborský

PLoS Comput. Biol., 2015

Rational design of α-helical tandem repeat proteins with closed architectures.

Lindsey Doyle, Jazmine Hallinan, Jill Bolduc, Fabio Parmeggiani, David Baker, Barry L. Stoddard, Philip Bradley

Nat., 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

Nat., 2015

Template Scoring Methods for Protein Torsion Angle Prediction.

Zafer Aydin, David Baker, William Stafford Noble

Proceedings of the Biomedical Engineering Systems and Technologies, 2015

Constructing Structural Profiles for Protein Torsion Angle Prediction.

Zafer Aydin, David Baker, William Stafford Noble

Proceedings of the BIOINFORMATICS 2015, 2015

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

Proc. Natl. Acad. Sci. USA, 2014

High-Resolution Modeling of Transmembrane Helical Protein Structures from Distant Homologues.

Kuang-Yui M. Chen, Jiaming Sun, Jason S. Salvo, David Baker, Patrick Barth

PLoS Comput. Biol., 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

Nat., 2014

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, Alexandria Schroeter, Man Chen, Skye MacPherson, Andreia M. Serra, Yumiko Adachi, Margaret A. Holmes, Yuxing Li, Rachel E. Klevit, Barney S. Graham, Richard T. Wyatt, David Baker, Roland K. Strong, James E. Crowe Jr., Philip R. Johnson, William R. Schief

Nat., 2014

2013

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

Nat., 2013

2012

Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers.

Michael D. Tyka, Kenneth Jung, David Baker

J. Comput. Chem., 2012

2011

Algorithm discovery by protein folding game players.

Firas Khatib, Seth Cooper, Michael D. Tyka, Kefan Xu, Ilya Makedon, Zoran Popovic, David Baker, Foldit players

Proc. Natl. Acad. Sci. USA, 2011

Analysis of social gameplay macros in the Foldit cookbook.

Seth Cooper, Firas Khatib, Ilya Makedon, Hao Lü, Janos Barbero, David Baker, James Fogarty, Zoran Popovic, Foldit players

Proceedings of the Foundations of Digital Games, 2011

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, Zoran Popovic, Foldit players

Nat., 2010

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, Zoran Popovic

Proceedings of the International Conference on the Foundations of Digital Games, 2010

2009

Computation of Conformational Coupling in Allosteric Proteins.

Brian A. Kidd, David Baker, Wendy E. Thomas

PLoS Comput. Biol., 2009

Structure similarity measure with penalty for close non-equivalent residues.

Ruslan Sadreyev, Shuoyong Shi, David Baker, Nick V. Grishin

Bioinform., 2009

2008

Advances in Rosetta protein structure prediction on massively parallel systems.

Srivatsan Raman, Bin Qian, David Baker, Ross C. Walker

IBM J. Res. Dev., 2008

2007

Feature Selection Methods for Improving Protein Structure Prediction with Rosetta.

Ben Blum, Michael I. Jordan, David E. Kim, Rhiju Das, Philip Bradley, David Baker

Proceedings of the Advances in Neural Information Processing Systems 20, 2007

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

Proceedings of the ACM/IEEE SC2006 Conference on High Performance Networking and Computing, 2006

Parallelization and performance characterization of protein 3D structure prediction of Rosetta.

Wenlong Li, Tao Wang, Eric Q. Li, David Baker, Li Jin, Steven Ge, Yurong Chen, Yimin Zhang

Proceedings of the 20th International Parallel and Distributed Processing Symposium (IPDPS 2006), 2006

2004

Protein structure prediction and analysis using the Robetta server.

David E. Kim, Dylan Chivian, David Baker

Nucleic Acids Res., 2004

Protein Structure Prediction Using Rosetta.

Carol A. Rohl, Charlie E. M. Strauss, Kira M. S. Misura, David Baker

Proceedings of the Numerical Computer Methods, Part D, 2004

2000

Detection of Protein Coding Sequences Using a Mixture Model for Local Protein Amino Acid Sequence.

Edward C. Thayer, Chris Bystroff, David Baker

J. Comput. Biol., 2000