David Baker

Publication Activity (10 Years)

Years Active: 1992-2024
Publications (10 Years): 29

Top Topics

Biological Sequences

Protein Structure

Subcellular Localization

Top Venues

PLoS Comput. Biol.

Publications

Sarah J. Wait, Marc Expòsit, Sophia Lin, Michael Rappleye, Justin Daho Lee, Samuel A. Colby, Lily Torp, Anthony Asencio, Annette Smith, Michael Regnier, Farid Moussavi-Harami, David Baker, Christina K. Kim, Andre Berndt
Machine learning-guided engineering of genetically encoded fluorescent calcium indicators. Nat. Comput. Sci. 4 (3) (2024)
Brian L. Trippe, Jason Yim, Doug Tischer, David Baker, Tamara Broderick, Regina Barzilay, Tommi S. Jaakkola
Diffusion Probabilistic Modeling of Protein Backbones in 3D for the motif-scaffolding problem. ICLR (2023)
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
Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock. PLoS Comput. Biol. 19 (5) (2023)
David Baker
. J. Libr. Inf. Sci. 54 (4) (2022)
Brian L. Trippe, Jason Yim, Doug Tischer, David Baker, Tamara Broderick, Regina Barzilay, Tommi Jaakkola
Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem. CoRR (2022)
Johannes Linder, Alyssa La Fleur, Zibo Chen, Ajasja Ljubetic, David Baker, Sreeram Kannan, Georg Seelig
Interpreting neural networks for biological sequences by learning stochastic masks. Nat. Mach. Intell. 4 (1) (2022)
Neeladri Sen, Ivan Anishchenko, Nicola Bordin, Ian Sillitoe, Sameer Velankar, David Baker, Christine A. Orengo
Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs. Briefings Bioinform. 23 (4) (2022)
Luca Turchet, David Baker, Tony Stockman
Musical Haptic Wearables for Synchronisation of Visually-impaired Performers: a Co-design Approach. IMX (2021)
Brian Coventry, David Baker
Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds. PLoS Comput. Biol. 17 (3) (2021)
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
Better together: Elements of successful scientific software development in a distributed collaborative community. PLoS Comput. Biol. 16 (5) (2020)
Qi Wu, Zhenling Peng, Ivan Anishchenko, Qian Cong, David Baker, Jianyi Yang
Protein contact prediction using metagenome sequence data and residual neural networks. Bioinform. 36 (1) (2020)
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
Programmable design of orthogonal protein heterodimers. Nat. 565 (7737) (2019)
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
De novo design of bioactive protein switches. Nat. 572 (7768) (2019)
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
De novo design of potent and selective mimics of IL-2 and IL-15. Nat. 565 (7738) (2019)
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
Modular and tunable biological feedback control using a de novo protein switch. Nat. 572 (7768) (2019)
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
De novo protein design by citizen scientists. Nat. 570 (7761) (2019)
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
De novo design of a fluorescence-activating β-barrel. Nat. 561 (7724) (2018)
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
Surrogate Wnt agonists that phenocopy canonical Wnt and β-catenin signalling. Nat. 545 (7653) (2017)
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
Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3. Nat. 548 (7667) (2017)
Robert Kleffner, Jeff Flatten, Andrew Leaver-Fay, David Baker, Justin B. Siegel, Firas Khatib, Seth Cooper
Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta. Bioinform. 33 (17) (2017)
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
protein design for targeted therapeutics. Nat. 550 (7674) (2017)
Edgar Berdahl, Michael Blandino, David Baker, Daniel Shanahan
An Approach for Using Information Theory to Investigate Continuous Control of Analog Sensors by Humans. Audio Mostly Conference (2016)
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
Corrigendum: Design of a hyperstable 60-subunit protein icosahedron. Nat. 540 (7631) (2016)
Ankit Agrawal, Jason Scott Mathias, David Baker, Alok N. Choudhary
Identifying hotspots in five year survival electronic health records of older adults. ICCABS (2016)
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
design of hyperstable constrained peptides. Nat. 538 (7625) (2016)
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
CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge. J. Chem. Inf. Model. 56 (6) (2016)
Ankit Agrawal, Jason Scott Mathias, David Baker, Alok N. Choudhary
Five Year Life Expectancy Calculator for Older Adults. ICDM Workshops (2016)
David Baker, Anna Clements, Catherine Grout, Simon Kerridge, Valerie McCutcheon, Helen Newnham
CASRAI-UK: Using the CASRAI Approach to Develop Standards for Communicating and Sharing Research Information in the UK. CRIS (2016)
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
Design of a hyperstable 60-subunit protein icosahedron. Nat. 535 (7610) (2016)
T. J. Brunette, Fabio Parmeggiani, Po-Ssu Huang, Gira Bhabha, Damian C. Ekiert, Susan E. Tsutakawa, Greg L. Hura, John A. Tainer, David Baker
Exploring the repeat protein universe through computational protein design. Nat. 528 (7583) (2015)
Lindsey Doyle, Jazmine Hallinan, Jill Bolduc, Fabio Parmeggiani, David Baker, Barry L. Stoddard, Philip Bradley
Rational design of α-helical tandem repeat proteins with closed architectures. Nat. 528 (7583) (2015)
Zafer Aydin, David Baker, William Stafford Noble
Template Scoring Methods for Protein Torsion Angle Prediction. BIOSTEC (Selected Papers) (2015)
David Bednar, Koen Beerens, Eva Sebestova, Jaroslav Bendl, Sagar D. Khare, Radka Chaloupkova, Zbynek Prokop, Jan Brezovsky, David Baker, Jirí Damborský
FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants. PLoS Comput. Biol. 11 (11) (2015)
Zafer Aydin, David Baker, William Stafford Noble
Constructing Structural Profiles for Protein Torsion Angle Prediction. BIOINFORMATICS (2015)
Laure Haak, David Baker, Thorsten Höllrigl
CASRAI and ORCID: Putting the Pieces together to Collaboratively Support the Research Community. CRIS (2014)
Chris King, Esteban N. Garza, Ronit Mazor, Jonathan L. Linehan, Ira Pastan, Marion Pepper, David Baker
Removing T-cell epitopes with computational protein design. Proc. Natl. Acad. Sci. USA 111 (23) (2014)
Neil P. King, Jacob B. Bale, William Sheffler, Dan E. McNamara, Shane Gonen, Tamir Gonen, Todd O. Yeates, David Baker
Accurate design of co-assembling multi-component protein nanomaterials. Nat. 510 (7503) (2014)
Brigitte Jörg, Thorsten Höllrigl, David Baker
Harmonising and Formalising Research Administration Profiles CASRAI / CERIF. CRIS (2014)
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
Proof of principle for epitope-focused vaccine design. Nat. 507 (7491) (2014)
Kuang-Yui M. Chen, Jiaming Sun, Jason S. Salvo, David Baker, Patrick Barth
High-Resolution Modeling of Transmembrane Helical Protein Structures from Distant Homologues. PLoS Comput. Biol. 10 (5) (2014)
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
Computational design of ligand-binding proteins with high affinity and selectivity. Nat. 501 (7466) (2013)
Laurel L. Haak, David Baker, Matthew A. Probus
Creating a Data Infrastructure for Tracking Knowledge Flow. CRIS (2012)
Michael D. Tyka, Kenneth Jung, David Baker
Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers. J. Comput. Chem. 33 (31) (2012)
David Baker, Tom Costello
Your Hollywood Guide to Antipatterns. IT Prof. 14 (3) (2012)
Hartmut Boesch, David Baker, Brian Connor, David Crisp, Charles E. Miller
Column Retrievals from Shortwave-Infrared Satellite Observations of the Orbiting Carbon Observatory-2 Mission. Remote. Sens. 3 (2) (2011)
Firas Khatib, Seth Cooper, Michael D. Tyka, Kefan Xu, Ilya Makedon, Zoran Popovic, David Baker, Foldit players
Algorithm discovery by protein folding game players. Proc. Natl. Acad. Sci. USA 108 (47) (2011)
Seth Cooper, Firas Khatib, Ilya Makedon, Hao Lü, Janos Barbero, David Baker, James Fogarty, Zoran Popovic, Foldit players
Analysis of social gameplay macros in the Foldit cookbook. FDG (2011)
Seth Cooper, Firas Khatib, Adrien Treuille, Janos Barbero, Jeehyung Lee, Michael Beenen, Andrew Leaver-Fay, David Baker, Zoran Popovic, Foldit players
Predicting protein structures with a multiplayer online game. Nat. 466 (7307) (2010)
Seth Cooper, Adrien Treuille, Janos Barbero, Andrew Leaver-Fay, Kathleen Tuite, Firas Khatib, Alex Cho Snyder, Michael Beenen, David Salesin, David Baker, Zoran Popovic
The challenge of designing scientific discovery games. FDG (2010)
Brian A. Kidd, David Baker, Wendy E. Thomas
Computation of Conformational Coupling in Allosteric Proteins. PLoS Comput. Biol. 5 (8) (2009)
Ruslan Sadreyev, Shuoyong Shi, David Baker, Nick V. Grishin
Structure similarity measure with penalty for close non-equivalent residues. Bioinform. 25 (10) (2009)
June Clark, Bernice Baker, David Baker
Getting eHealth into Basic Nursing Education: Report of the RCN Information in Nursing Project. Nursing Informatics (2009)
Srivatsan Raman, Bin Qian, David Baker, Ross C. Walker
Advances in Rosetta protein structure prediction on massively parallel systems. IBM J. Res. Dev. 52 (1-2) (2008)
Ben Blum, Michael I. Jordan, David Kim, Rhiju Das, Philip Bradley, David Baker
Feature Selection Methods for Improving Protein Structure Prediction with Rosetta. NIPS (2007)
Ross C. Walker, Srivatsan Raman, David Baker
Poster reception - High resolution, high throughput protein structure prediction using IBM Blue Gene supercomputers: predicting CASP targets in record time. SC (2006)
Matthew L. Baker, Wen Jiang, William J. Wedemeyer, Frazer J. Rixon, David Baker, Wah Chiu
Ab Initio Modeling of the Herpesvirus VP26 Core Domain Assessed by CryoEM Density. PLoS Comput. Biol. 2 (10) (2006)
David E. Kim, Dylan Chivian, David Baker
Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Edward C. Thayer, Chris Bystroff, David Baker
Detection of Protein Coding Sequences Using a Mixture Model for Local Protein Amino Acid Sequence. J. Comput. Biol. 7 (1-2) (2000)
David Baker
A whole new ballgame - supercomputing on two AA batteries (keynote session). MICRO (2000)
David Baker
The multimedia librarian in the twenty-first century: the viewpoint of a university librarian. OCLC Syst. Serv. 15 (1) (1999)
David Baker
Resource Allocation in University Libraries. J. Documentation 48 (1) (1992)
David Baker, Russell F. Haddleton, Kevin G. Wika
A Distributed Scheduling Simulation. HPDC (1992)