David Baker

46 papers A* 1A 2C 2Journal 37Unranked 3
YearRankTypeTitle / Venue / Authors
2023 A* conf
Diffusion Probabilistic Modeling of Protein Backbones in 3D for the motif-scaffolding problem.
ICLR
Brian L. Trippe, Jason Yim, Doug Tischer, David Baker, Tamara Broderick, Regina Barzilay, Tommi S. Jaakkola
2023 J jnl
Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock.
PLoS Comput. Biol.
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
2022 J jnl
Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs.
Briefings Bioinform.
Neeladri Sen, Ivan Anishchenko, Nicola Bordin, Ian Sillitoe, Sameer Velankar, David Baker, Christine A. Orengo
2022 J jnl
Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem.
CoRR
Brian L. Trippe, Jason Yim, Doug Tischer, David Baker, Tamara Broderick, Regina Barzilay, Tommi S. Jaakkola
2022 J jnl
Interpreting neural networks for biological sequences by learning stochastic masks.
Nat. Mach. Intell.
Johannes Linder, Alyssa La Fleur, Zibo Chen, Ajasja Ljubetic, David Baker, Sreeram Kannan, Georg Seelig
2021 J jnl
Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds.
PLoS Comput. Biol.
Brian Coventry, David Baker
2020 J jnl
Better together: Elements of successful scientific software development in a distributed collaborative community.
PLoS Comput. Biol.
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
2020 J jnl
Protein contact prediction using metagenome sequence data and residual neural networks.
Bioinform.
Qi Wu, Zhenling Peng, Ivan Anishchenko, Qian Cong, David Baker, Jianyi Yang
2019 J jnl
De novo design of bioactive protein switches.
Nat.
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
2019 J jnl
De novo design of potent and selective mimics of IL-2 and IL-15.
Nat.
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
2019 J jnl
De novo protein design by citizen scientists.
Nat.
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
2019 J jnl
Modular and tunable biological feedback control using a de novo protein switch.
Nat.
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
2019 J jnl
Programmable design of orthogonal protein heterodimers.
Nat.
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
2018 J jnl
De novo design of a fluorescence-activating β-barrel.
Nat.
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
2017 J jnl
Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3.
Nat.
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
2017 J jnl
Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta.
Bioinform.
Robert Kleffner, Jeff Flatten, Andrew Leaver-Fay, David Baker, Justin B. Siegel, Firas Khatib, Seth Cooper
2017 J jnl
Massively parallel
Nat.
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
2017 J jnl
Surrogate Wnt agonists that phenocopy canonical Wnt and β-catenin signalling.
Nat.
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
2016 J jnl
Accurate
Nat.
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
2016 J jnl
CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge.
J. Chem. Inf. Model.
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
2016 J jnl
Corrigendum: Design of a hyperstable 60-subunit protein icosahedron.
Nat.
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
2016 J jnl
Design of a hyperstable 60-subunit protein icosahedron.
Nat.
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
2015 — conf
Constructing Structural Profiles for Protein Torsion Angle Prediction.
BIOINFORMATICS
Zafer Aydin, David Baker, William Stafford Noble
2015 J jnl
Exploring the repeat protein universe through computational protein design.
Nat.
T. J. Brunette, Fabio Parmeggiani, Po-Ssu Huang, Gira Bhabha, Damian C. Ekiert, Susan E. Tsutakawa, Greg L. Hura, John A. Tainer, David Baker
2015 J jnl
FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants.
PLoS Comput. Biol.
David Bednar, Koen Beerens, Eva Sebestova, Jaroslav Bendl, Sagar D. Khare, Radka Chaloupkova, Zbynek Prokop, Jan Brezovsky, David Baker, Jirí Damborský
2015 J jnl
Rational design of α-helical tandem repeat proteins with closed architectures.
Nat.
Lindsey Doyle, Jazmine Hallinan, Jill Bolduc, Fabio Parmeggiani, David Baker, Barry L. Stoddard, Philip Bradley
2015 — conf
Template Scoring Methods for Protein Torsion Angle Prediction.
BIOSTEC (Selected Papers)
Zafer Aydin, David Baker, William Stafford Noble
2014 J jnl
Accurate design of co-assembling multi-component protein nanomaterials.
Nat.
Neil P. King, Jacob B. Bale, William Sheffler, Dan E. McNamara, Shane Gonen, Tamir Gonen, Todd O. Yeates, David Baker
2014 J jnl
High-Resolution Modeling of Transmembrane Helical Protein Structures from Distant Homologues.
PLoS Comput. Biol.
Kuang-Yui M. Chen, Jiaming Sun, Jason S. Salvo, David Baker, Patrick Barth
2014 J jnl
Proof of principle for epitope-focused vaccine design.
Nat.
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
2014 J jnl
Removing T-cell epitopes with computational protein design.
Proc. Natl. Acad. Sci. USA
Chris King, Esteban N. Garza, Ronit Mazor, Jonathan L. Linehan, Ira Pastan, Marion Pepper, David Baker
2013 J jnl
Computational design of ligand-binding proteins with high affinity and selectivity.
Nat.
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
2012 J jnl
Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers.
J. Comput. Chem.
Michael D. Tyka, Kenneth Jung, David Baker
2011 J jnl
Algorithm discovery by protein folding game players.
Proc. Natl. Acad. Sci. USA
Firas Khatib, Seth Cooper, Michael D. Tyka, Kefan Xu, Ilya Makedon, Zoran Popovic, David Baker, Foldit players
2011 C conf
Analysis of social gameplay macros in the Foldit cookbook.
FDG
Seth Cooper, Firas Khatib, Ilya Makedon, Hao Lü, Janos Barbero, David Baker, James Fogarty, Zoran Popovic, Foldit players
2010 J jnl
Predicting protein structures with a multiplayer online game.
Nat.
Seth Cooper, Firas Khatib, Adrien Treuille, Janos Barbero, Jeehyung Lee, Michael Beenen, Andrew Leaver-Fay, David Baker, Zoran Popovic, Foldit players
2010 C conf
The challenge of designing scientific discovery games.
FDG
Seth Cooper, Adrien Treuille, Janos Barbero, Andrew Leaver-Fay, Kathleen Tuite, Firas Khatib, Alex Cho Snyder, Michael Beenen, David Salesin, David Baker, Zoran Popovic
2009 J jnl
Computation of Conformational Coupling in Allosteric Proteins.
PLoS Comput. Biol.
Brian A. Kidd, David Baker, Wendy E. Thomas
2009 J jnl
Structure similarity measure with penalty for close non-equivalent residues.
Bioinform.
Ruslan Sadreyev, Shuoyong Shi, David Baker, Nick V. Grishin
2008 J jnl
Advances in Rosetta protein structure prediction on massively parallel systems.
IBM J. Res. Dev.
Srivatsan Raman, Bin Qian, David Baker, Ross C. Walker
2007 — conf
Feature Selection Methods for Improving Protein Structure Prediction with Rosetta.
NIPS
Ben Blum, Michael I. Jordan, David E. Kim, Rhiju Das, Philip Bradley, David Baker
2006 A conf
Parallelization and performance characterization of protein 3D structure prediction of Rosetta.
IPDPS
Wenlong Li, Tao Wang, Eric Q. Li, David Baker, Li Jin, Steven Ge, Yurong Chen, Yimin Zhang
2006 A conf
Poster reception - High resolution, high throughput protein structure prediction using IBM Blue Gene supercomputers: predicting CASP targets in record time.
SC
Ross C. Walker, Srivatsan Raman, David Baker
2004 — ch.
Protein Structure Prediction Using Rosetta.
Numerical Computer Methods, Part D
Carol A. Rohl, Charlie E. M. Strauss, Kira M. S. Misura, David Baker
2004 J jnl
Protein structure prediction and analysis using the Robetta server.
Nucleic Acids Res.
David E. Kim, Dylan Chivian, David Baker
2000 J jnl
Detection of Protein Coding Sequences Using a Mixture Model for Local Protein Amino Acid Sequence.
J. Comput. Biol.
Edward C. Thayer, Chris Bystroff, David Baker