David Baker

David Baker, Kevin G. Wika, Russell F. Haddleton, 1992, Proceedings of the First International Symposium on High-Performance Distributed Computing. (HPDC-1).

Evolution of a designed protein assembly encapsulating its own RNA genome

David Baker, Neil P. King, Jacob B. Bale, 2017, Nature.

Feature space resampling for protein conformational search

Michael I. Jordan, David Baker, Michael I Jordan, 2010, Proteins.

David Baker, Nick V. Grishin, Ruslan Sadreyev, 2009, Bioinform..

Computational protein design with rosetta

David Baker, Ingemar André, 2008 .

Programmable design of orthogonal protein heterodimers

David Baker, Vikram Khipple Mulligan, Frank DiMaio, 2018, Nature.

Feature Selection Methods for Improving Protein Structure Prediction with Rosetta

David Kim, Michael I. Jordan, David Baker, 2007, NIPS.

Improved beta‐protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation

David Baker, Philip Bradley, P. Bradley, 2006, Proteins.

Ab Initio Modeling of the Herpesvirus VP26 Core Domain Assessed by CryoEM Density

Matthew L. Baker, David Baker, Wah Chiu, 2006, PLoS Comput. Biol..

Global Characterization of CO2 Column Retrievals from Shortwave-Infrared Satellite Observations of the Orbiting Carbon Observatory-2 Mission

Hartmut Boesch, David Crisp, David Baker, 2011, Remote. Sens..

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.

Jens Meiler, Florian Richter, David Baker, 2011, Methods in enzymology.

Identifying hotspots in five year survival electronic health records of older adults

Alok N. Choudhary, David Baker, Ankit Agrawal, 2016, 2016 IEEE 6th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS).

Harmonising and Formalising Research Administration Profiles CASRAI / CERIF

David Baker, Thorsten Höllrigl, Brigitte Jörg, 2014, CRIS.

Evaluation and optimization of discrete state models of protein folding.

Oliver F. Lange, David Baker, Oliver F Lange, 2012, The journal of physical chemistry. B.

1SB-01 Computational De Novo Design of Protein Structures(1SB Exploring design principles of life,The 49th Annual Meeting of the Biophysical Society of Japan)

David Baker, Gaohua Liu, Gaetano T. Montelione, 2011 .

Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation.

David Baker, Angel R Ortiz, Bin Qian, 2004, Proceedings of the National Academy of Sciences of the United States of America.

An Approach for Using Information Theory to Investigate Continuous Control of Analog Sensors by Humans

David Baker, Edgar Berdahl, Daniel Shanahan, 2016, Audio Mostly Conference.

Computation of Conformational Coupling in Allosteric Proteins

David Baker, Brian A. Kidd, Wendy E. Thomas, 2009, PLoS Comput. Biol..

A Structural Biology and Protein Engineering Approach to the Engineering Highly Proficient Catalytic Bioscavengers for In Vivo Detoxification of a Broad Spectrum of Nerve Agents

David Baker, Joel L. Sussman, Dan S. Tawfik, 2016 .

Five Year Life Expectancy Calculator for Older Adults

Alok N. Choudhary, David Baker, Ankit Agrawal, 2016, 2016 IEEE 16th International Conference on Data Mining Workshops (ICDMW).

Community-wide assessment of protein-interface modeling suggests improvements to design methodology.

Kengo Kinoshita, Haruki Nakamura, Genki Terashi, 2011, Journal of molecular biology.

Ranking predicted protein structures with support vector regression

David Baker, William Stafford Noble, Jian Qiu, 2007, Proteins.

CASRAI and ORCID: Putting the Pieces together to Collaboratively Support the Research Community

David Baker, Thorsten Höllrigl, Laurel L. Haak, 2014, CRIS.

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

David Baker, Kenneth Jung, Michael D. Tyka, 2012, J. Comput. Chem..

Rational design of alpha-helical tandem repeat proteins with closed architectures

David Baker, Barry L. Stoddard, Fabio Parmeggiani, 2015, Nature.

Automated prediction of CASP‐5 structures using the Robetta server

Lars Malmström, David Baker, Timothy Robertson, 2003, Proteins.

WeFold: A coopetition for protein structure prediction

Adam Liwo, Yi He, David Baker, 2014, Proteins.

Structure Prediction using Coevolution

David Baker, David E. Kim, Sergey Ovchinnikov, 2015 .

Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation

Jens Meiler, David Baker, Dylan Chivian, 2003, Proteins.

Prediction of CASP6 structures using automated robetta protocols

Lars Malmström, David Baker, Dylan Chivian, 2005, Proteins.

CASRAI-UK: Using the CASRAI Approach to Develop Standards for Communicating and Sharing Research Information in the UK

David Baker, Simon Kerridge, Valerie McCutcheon, 2016, CRIS.

The dual role of fragments in fragment‐assembly methods for de novo protein structure prediction

David Baker, Robert Vernon, Julia Handl, 2012, Proteins.

Template Scoring Methods for Protein Torsion Angle Prediction

Zafer Aydin, David Baker, William Stafford Noble, 2015, BIOSTEC.

Recognition of Leitmotives in Richard Wagner's Music: An Item Response Theory Approach

David Baker, Daniel Müllensiefen, Tim Crawford, 2014, ECDA.

Enabling Prediction for Optimal Fuel Economy Vehicle Control

Farnoush Banaei-Kashani, David Baker, Thomas H. Bradley, 2018 .

Combining Crystallographic and Structure-Modeling Approaches in Macromolecular Crystallography

Randy J. Read, Paul D. Adams, David Baker, 2014 .

A whole new ballgame—supercomputing on two AA batteries (keynote session)

David Baker, 2000, MICRO 33.

Advances, Interactions, and Future Developments in the CNS, Phenix, and Rosetta Structural Biology Software Systems Annual Review of Biophysics

Randy J. Read, Paul D. Adams, David Baker, 2012 .

Protein structure prediction and analysis using the Robetta server

David Baker, Dylan Chivian, David E. Kim, 2004, Nucleic Acids Res..

Corrigendum: Design of a hyperstable 60-subunit protein icosahedron

David Baker, Neil P. King, William Sheffler, 2016, Nature.

The multimedia librarian in the twenty-first century: the viewpoint of a university librarian

David Baker, 1999, OCLC Syst. Serv..

Resource Allocation in University Libraries

David Baker, 1992, J. Documentation.

Automating human intuition for protein design

David Baker, Chris King, Lucas G Nivón, 2014, Proteins.

Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems.

David Baker, Randy J Read, Frank DiMaio, 2013, Annual review of biophysics.

Protein Structure Prediction Using Rosetta

David Baker, Charlie E M Strauss, Carol A Rohl, 2004, Numerical Computer Methods, Part D.

Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: Four approaches that performed well in CASP8

Keehyoung Joo, Jinwoo Lee, Jooyoung Lee, 2009, Proteins.

Structure prediction for CASP8 with all‐atom refinement using Rosetta

Oliver F. Lange, David Kim, Nick V Grishin, 2009, Proteins.

Creating a Data Infrastructure for Tracking Knowledge Flow

David Baker, Laurel L. Haak, Matthew A. Probus, 2012, CRIS.

Protein-protein docking with backbone flexibility.

David Baker, Chu Wang, Philip Bradley, 2007, Journal of molecular biology.

Reporting@Home: Delivering Dynamic Graphical Feedback to Participants and Researchers in Community Computing Projects

Stuart Ozer, David Baker, David E. Kim, 2007 .

Advances in Rosetta protein structure prediction on massively parallel systems

David Baker, Bin Qian, Ross C. Walker, 2008, IBM J. Res. Dev..

Accurate de novo design of hyperstable constrained peptides

David Baker, James M. Olson, Thomas Szyperski, 2016, Nature.

Getting eHealth into Basic Nursing Education: Report of the RCN Information in Nursing Project

David Baker, June Clark, Bernice Baker, 2009, Nursing Informatics.

Assessment of predictions submitted for the CASP7 domain prediction category

David Kim, Keehyoung Joo, Jinwoo Lee, 2007, Proteins.

Macromolecular modeling with rosetta.

David Baker, Rhiju Das, D. Baker, 2008, Annual review of biochemistry.

Computational design of a homotrimeric metalloprotein with a trisbipyridyl core

David Baker, William Sheffler, Peter H Zwart, 2016, Proceedings of the National Academy of Sciences.

The origin of consistent protein structure refinement from structural averaging.

David Baker, Frank DiMaio, Hahnbeom Park, 2015, Structure.

Structural and kinetic characterization of the simplified SH3 domain FP1

David Baker, D. Baker, R. Klevit, 2003, Protein science : a publication of the Protein Society.

Control of repeat protein curvature by computational protein design

David Baker, Barry L. Stoddard, Keunwan Park, 2014, Nature Structural &Molecular Biology.

Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series.

David Baker, Orly Dym, Colin J Jackson, 2010, Journal of molecular biology.

Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases

David Baker, Patrick Danaher, Barry L. Stoddard, 2012, Nucleic acids research.

A novel semi-biosynthetic route for artemisinin production using engineered substrate-promiscuous P450(BM3).

David Baker, Jay D Keasling, Yasuo Yoshikuni, 2009, ACS chemical biology.

A phage display system for studying the sequence determinants of protein folding

David Baker, D. Baker, D. Riddle, 1995, Protein science : a publication of the Protein Society.

De novo protein design by deep network hallucination

David Baker, Ivan Anishchenko, Sergey Ovchinnikov, 2020, Nature.

Bioluminescent sensor proteins for point-of-care therapeutic drug monitoring.

David Baker, Luc Patiny, Alberto Schena, 2014, Nature chemical biology.

megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering

David Baker, Jay Shendure, Barry L. Stoddard, 2013, Nucleic acids research.

Comprehensive computational design of ordered peptide macrocycles

David Baker, Joshua N. Adkins, Gabriele Varani, 2017, Science.

Evaluation and ranking of enzyme designs

David Baker, Gert Kiss, K N Houk, 2010, Protein science : a publication of the Protein Society.

High-throughput characterization of protein–protein interactions by reprogramming yeast mating

David Baker, Eric Klavins, D. Baker, 2017, Proceedings of the National Academy of Sciences.

Selective targeting of engineered T cells using orthogonal IL-2 cytokine-receptor complexes

David Baker, Antoni Ribas, Indigo C King, 2018, Science.

Optimization of the In-silico-designed Kemp Eliminase Ke70 by Computational Design and Directed Evolution Journal of Molecular Biology

David Baker, Orly Dym, Andrew M Wollacott, 2022 .

Rosetta in CAPRI rounds 13–19

David Baker, Sarel J Fleishman, Rhiju Das, 2010, Proteins.

Improved molecular replacement by density- and energy-guided protein structure optimization

Randy J. Read, David Baker, Deborah Fass, 2011, Nature.

Symmetry recognizing asymmetry: analysis of the interactions between the C-type lectin-like immunoreceptor NKG2D and MHC class I-like ligands.

David Baker, Tanja Kortemme, D. Baker, 2003, Structure.

Solution structure of a minor and transiently formed state of a T4 lysozyme mutant

Oliver F. Lange, David Baker, Bruno E. Correia, 2011, Nature.

Searching for folded proteins in vitro and in silico.

David Baker, D. Baker, Alexander L Watters, 2004, European journal of biochemistry.

Simple physical models connect theory and experiment in protein folding kinetics.

David Baker, Tanja Kortemme, Alexandre V Morozov, 2002, Journal of molecular biology.

Computational design of trimeric influenza neutralizing proteins targeting the hemagglutinin receptor binding site

David Baker, William Sheffler, Paul Yager, 2017, Nature Biotechnology.

De novo protein structure determination from near-atomic resolution cryo-EM maps

David Baker, Frank DiMaio, Mikhail Kudryashev, 2015, Nature Methods.

Incorporation of evolutionary information into Rosetta comparative modeling

David Baker, D. Baker, James M Thompson, 2011, Proteins.

Blind docking of pharmaceutically relevant compounds using RosettaLigand

David Baker, Kaushik Raha, Ian W. Davis, 2009, Protein science : a publication of the Protein Society.

High-resolution structural validation of the computational redesign of human U1A protein.

David Baker, Gabriele Varani, Neil Dobson, 2006, Structure.

De novo design of self-assembling helical protein filaments.

David Baker, William Sheffler, Linda Wordeman, 2018 .

Remodeling a β-peptide bundle

David Baker, Rhiju Das, Fang-Chieh Chou, 2013 .

Enantioselective enzymes by computational design and in silico screening.

David Baker, Siewert J Marrink, Hein J Wijma, 2015, Angewandte Chemie.

Discovery and engineering of enhanced SUMO protease enzymes

David Baker, Lauren P. Carter, Christopher D. Lima, 2018, The Journal of Biological Chemistry.

Increased Diels-Alderase Activity through Foldit Player Guided Backbone Remodeling

David Baker, Zoran Popovic, Jacob B. Bale, 2012, Nature Biotechnology.

Experiment and theory highlight role of native state topology in SH3 folding

David Baker, Ingo Ruczinski, D. Baker, 1999, Nature Structural Biology.

Exploration of alternate catalytic mechanisms and optimization strategies for retroaldolase design.

David Baker, Liang Tong, Donald Hilvert, 2014, Journal of molecular biology.

Contact order revisited: Influence of protein size on the folding rate

Kevin W Plaxco, David Baker, Dmitry N Ivankov, 2003, Protein science : a publication of the Protein Society.

Computer-based redesign of a protein folding pathway

David Baker, Brian Kuhlman, D. Baker, 2001, Nature Structural Biology.

A Pareto-Optimal Refinement Method for Protein Design Scaffolds

David Baker, Rocco Moretti, D. Baker, 2013, PloS one.

Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59

David Baker, Orly Dym, Kendall N Houk, 2012, Proceedings of the National Academy of Sciences.

A new twist in TCR diversity revealed by a forbidden alphabeta TCR.

David Baker, Tanja Kortemme, Sarel J Fleishman, 2008, Journal of molecular biology.

Computational Design of an α-Gliadin Peptidase

David Baker, Justin B. Siegel, Jeremy H. Mills, 2012, Journal of the American Chemical Society.

Ab initio methods.

David Baker, Richard Bonneau, Dylan Chivian, 2003, Methods of biochemical analysis.

proteins STRUCTURE O FUNCTION O BIOINFORMATICS Improving NMR protein structure quality by Rosetta refinement: A molecular

David Baker, Michael A Kennedy, Gaetano T Montelione, 2022 .

Using chlorophyll fluorescence to assess the fraction of absorbed light allocated to thermal dissipa

David Baker, David R. Bowling, D. Baker, 2008 .

PROTEINS: Structure, Function, and Bioinformatics 58:893–904 (2005) A “Solvated Rotamer ” Approach to Modeling Water- Mediated Hydrogen Bonds at Protein–Protein Interfaces

David Baker, Tanja Kortemme, Brian Kuhlman, 2022 .

Role of the Biomolecular Energy Gap in Protein Design, Structure, and Evolution

David Baker, Sarel J. Fleishman, D. Baker, 2012, Cell.

Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection.

David Baker, D. Baker, M. Scalley‐Kim, 2004, Journal of molecular biology.

A general computational approach for repeat protein design.

David Baker, Gaetano T Montelione, Keunwan Park, 2015, Journal of molecular biology.

Recapitulation and design of protein binding peptide structures and sequences.

David Baker, D. Baker, Vanita D Sood, 2006, Journal of molecular biology.

Modeling Disordered Regions in Proteins Using Rosetta

David Baker, William Sheffler, Michael Tyka, 2011, PloS one.

Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction.

David Baker, Alexandre V Morozov, Kira M S Misura, 2004, Journal of molecular biology.

Multiplex pairwise assembly of array-derived DNA oligonucleotides

David Baker, Jay Shendure, Marc J. Lajoie, 2015, Nucleic acids research.

Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition.

David Baker, Patrick Ernst, Andreas Plückthun, 2016, Journal of molecular biology.

Active Site Plasticity of a Computationally Designed Retro‐Aldolase Enzyme

David Baker, Donald Hilvert, D. Hilvert, 2014 .

Protein structure determination from pseudocontact shifts using ROSETTA.

David Baker, Thomas Huber, Gottfried Otting, 2012, Journal of molecular biology.

Computation and Functional Studies Provide a Model for the Structure of the Zinc Transporter hZIP4*

David Baker, Sergey Ovchinnikov, Hetunandan Kamisetty, 2015, The Journal of Biological Chemistry.

Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design.

David Baker, Donald Hilvert, Eric A. Althoff, 2011, Journal of molecular biology.

Mutations Designed to Destabilize the Receptor-Bound Conformation Increase MICA-NKG2D Association Rate and Affinity*

David Baker, Tanja Kortemme, T. Kortemme, 2007, Journal of Biological Chemistry.

Extreme stability in de novo-designed repeat arrays is determined by unusually stable short-range interactions

David Baker, Doug Barrick, Fabio Parmeggiani, 2018, Proceedings of the National Academy of Sciences.

A de novo protein binding pair by computational design and directed evolution.

David Baker, Orly Dym, Tamar Unger, 2011, Molecular cell.

Protein structure prediction for the male-specific region of the human Y chromosome.

Leszek Rychlewski, Nick V Grishin, David Baker, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Hotspot-centric de novo design of protein binders.

David Baker, Sarel J Fleishman, John Karanicolas, 2011, Journal of molecular biology.

Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis.

Ryo Takeuchi, David Baker, Joel L Sussman, 2012, Nature chemical biology.

A general strategy to construct small molecule biosensors

David Baker, Xavier Rios, George M Church, 2017 .

Crystal structure of a monomeric retroviral protease solved by protein folding game players

David Baker, Seth Cooper, Frank DiMaio, 2012, Nature Structural &Molecular Biology.

Quantitative reactivity profiling predicts functional cysteines in proteomes

David Baker, Benjamin F. Cravatt, Sagar Khare, 2010, Nature.

Sampling and energy evaluation challenges in ligand binding protein design

David Baker, Barry L. Stoddard, Hahnbeom Park, 2017, Protein science : a publication of the Protein Society.

Convergent mechanisms for recognition of divergent cytokines by the shared signaling receptor gp130.

David Baker, Tanja Kortemme, D. Baker, 2003, Molecular cell.

Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures

David Baker, Binchen Mao, Gaetano T. Montelione, 2014, Journal of the American Chemical Society.

The NMR–Rosetta capsid model of M13 bacteriophage reveals a quadrupled hydrophobic packing epitope

David Baker, Nikolaos G Sgourakis, D. Baker, 2015, Proceedings of the National Academy of Sciences.

Structure of the Type VI Secretion System Contractile Sheath

David Baker, Sebastian Scherer, Frank DiMaio, 2015, Cell.

Computational design of environmental sensors for the potent opioid fentanyl

David Baker, Matthew J Bick, Kai Johnsson, 2017, eLife.

A Computationally Designed Hemagglutinin Stem-Binding Protein Provides In Vivo Protection from Influenza Independent of a Host Immune Response

David Baker, Andrew B. Ward, Ian A. Wilson, 2016, PLoS pathogens.

De Novo Enzyme Design Using Rosetta3

David Baker, Andrew Leaver-Fay, Sagar D. Khare, 2011, PloS one.

Intrinsic disorder drives N-terminal ubiquitination by Ube2w

David Baker, Vinayak Vittal, Rachel E. Klevit, 2014, Nature chemical biology.

Computational design of a pH-sensitive IgG binding protein

David Baker, Sarel J Fleishman, Eva-Maria Strauch, 2013, Proceedings of the National Academy of Sciences.

Origins of coevolution between residues distant in protein 3D structures

David Baker, Ivan Anishchenko, Sergey Ovchinnikov, 2017, Proceedings of the National Academy of Sciences.

New algorithms and an in silico benchmark for computational enzyme design

Jens Meiler, David Baker, Eric A. Althoff, 2006, Protein science : a publication of the Protein Society.

A conserved structural motif mediates formation of the periplasmic rings in the type III secretion system

David Baker, Ingemar André, Wanyin Deng, 2009, Nature Structural &Molecular Biology.

Contributions of amino acid side chains to the kinetics and thermodynamics of the bivalent binding of protein L to Ig kappa light chain.

David Baker, Tanja Kortemme, David E. Kim, 2004, Biochemistry.

Low free energy cost of very long loop insertions in proteins

David Baker, Philippe Minard, D. Baker, 2003, Protein science : a publication of the Protein Society.

Experimental and computational analyses of the energetic basis for dual recognition of immunity proteins by colicin endonucleases.

David Baker, Colin Kleanthous, D. Baker, 2008, Journal of molecular biology.

Assessment of the optimization of affinity and specificity at protein–DNA interfaces

David Baker, Justin Ashworth, D. Baker, 2009, Nucleic acids research.

Prediction of structures of zinc‐binding proteins through explicit modeling of metal coordination geometry

David Baker, Michael Tyka, Chu Wang, 2010, Protein science : a publication of the Protein Society.

Designing Two-Dimensional Protein Arrays through Fusion of Multimers and Interface Mutations.

David Baker, Frank DiMaio, J. J. Richards, 2015, Nano letters.

Reprogramming homing endonuclease specificity through computational design and directed evolution

David Baker, Justin Ashworth, Tony Nolan, 2013, Nucleic acids research.

Motif‐directed flexible backbone design of functional interactions

David Baker, James J Havranek, D. Baker, 2009, Protein science : a publication of the Protein Society.

A Computationally Designed Inhibitor of an Epstein-Barr Viral Bcl-2 Protein Induces Apoptosis in Infected Cells

David Baker, Barry L. Stoddard, Bruno E. Correia, 2014, Cell.

Structural genomics of pathogenic protozoa: an overview.

David Baker, Thomas Earnest, Jürgen Bosch, 2008, Methods in molecular biology.

Prospects for de novo phasing with de novo protein models

David Baker, Rhiju Das, D. Baker, 2009, Acta crystallographica. Section D, Biological crystallography.

Origins of catalysis by computationally designed retroaldolase enzymes

David Baker, Daniel Herschlag, Jonathan K. Lassila, 2010, Proceedings of the National Academy of Sciences.

A New Twist in TCR Diversity Revealed by a Forbidden αβ TCR

David Baker, Sarel J. Fleishman, Tanja Kortemme, 2008 .

Cooperative hydrogen bonding in amyloid formation

David Baker, David Eisenberg, Lukasz Goldschmidt, 2007, Protein science : a publication of the Protein Society.

Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination.

David Baker, Anastassia N Alexandrova, William L Jorgensen, 2008, Journal of the American Chemical Society.

A cell-free platform for the prenylation of natural products and application to cannabinoid production

David Baker, Robert E. Taylor, James U. Bowie, 2019, Nature Communications.

CASP6 assessment of contact prediction

Jens Meiler, Alfonso Valencia, Marco Punta, 2005, Proteins.

Evaluation of Models of Electrostatic Interactions in Proteins

David Baker, Alexandre V. Morozov, Tanja Kortemme, 2003 .

Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation

David Baker, Oliver F Lange, D. Baker, 2011, Proteins.

Computational Design of Transmembrane Pores

David Baker, Frank DiMaio, Yang Hsia, 2020, Nature.

Induction of Potent Neutralizing Antibody Responses by a Designed Protein Nanoparticle Vaccine for Respiratory Syncytial Virus

David Baker, Neil P. King, Colin E. Correnti, 2019, Cell.

Increasing public involvement in structural biology.

David Baker, Seth Cooper, Firas Khatib, 2013, Structure.

Interactions of the Transmembrane Polymeric Rings of the Salmonella enterica Serovar Typhimurium Type III Secretion System

David Baker, David R. Goodlett, Tamir Gonen, 2010, mBio.

Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide‐rich de novo designed peptides

David Baker, Thomas Szyperski, Victor Ovchinnikov, 2018, Protein science : a publication of the Protein Society.

A computationally engineered RAS rheostat reveals RAS/ERK signaling dynamics

David Baker, Alejandro Wolf-Yadlin, Inna Goreshnik, 2016, Nature chemical biology.

Unique double-ring structure of the peroxisomal Pex1/Pex6 ATPase complex revealed by cryo-electron microscopy

David Baker, Frank DiMaio, Pawel A Penczek, 2015, Proceedings of the National Academy of Sciences.

Rapid online buffer exchange for screening of proteins, protein complexes and cell lysates by native mass spectrometry

David Baker, Zibo Chen, Scott E. Boyken, 2020, Nature Protocols.

Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase

David Baker, Clemens Mayer, Donald Hilvert, 2014, Proceedings of the National Academy of Sciences.

Structural basis for gating charge movement in the voltage sensor of a sodium channel

David Baker, William A Catterall, Vladimir Yarov-Yarovoy, 2011, Proceedings of the National Academy of Sciences.

Metastable states and folding free energy barriers

David Baker, 1998, Nature Structural Biology.

Structure of Lmaj006129AAA, a hypothetical protein from Leishmania major.

David Baker, Oleksandr Kalyuzhniy, Ethan A Merritt, 2006, Acta crystallographica. Section F, Structural biology and crystallization communications.

Comparison of designed and randomly generated catalysts for simple chemical reactions

David Baker, D. Baker, Yakov Kipnis, 2012, Protein science : a publication of the Protein Society.

Structure prediction using sparse simulated NOE restraints with Rosetta in CASP11

David Baker, Hahnbeom Park, Sergey Ovchinnikov, 2016, Proteins.

Crystal structure of XMRV protease differs from the structures of other retropepsins

David Baker, Frank DiMaio, Zbigniew Dauter, 2010, Nature Structural &Molecular Biology.

Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain

David Baker, D. Baker, D. Riddle, 1998, Nature Structural &Molecular Biology.

Evolution of a designed retro-aldolase leads to complete active site remodeling

David Baker, Donald Hilvert, Peter Kast, 2013, Nature chemical biology.

Accurate Automated Protein NMR Structure Determination Using Unassigned NOESY Data

David Baker, Gaohua Liu, Binchen Mao, 2009, Journal of the American Chemical Society.

Cloning, expression, purification, crystallization and preliminary X-ray diffraction data of the Pyrococcus horikoshii RadA intein.

David Baker, Frank DiMaio, Alexander Wlodawer, 2011, Acta crystallographica. Section F, Structural biology and crystallization communications.

Exploring folding free energy landscapes using computational protein design.

David Baker, Brian Kuhlman, D. Baker, 2004, Current opinion in structural biology.

Rational Design of Intercellular Adhesion Molecule-1 (ICAM-1) Variants for Antagonizing Integrin Lymphocyte Function-associated Antigen-1-dependent Adhesion*

David Baker, Tanja Kortemme, G. A. Lazar, 2006, Journal of Biological Chemistry.

Accurate design of megadalton-scale two-component icosahedral protein complexes

David Baker, Neil P. King, William Sheffler, 2016, Science.

De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures

David Baker, Vikram Khipple Mulligan, Haifan Wu, 2017, Proceedings of the National Academy of Sciences.

Regulatory DNA keyholes enable specific and persistent multi-gene expression programs in primary T cells without genome modification

David Baker, John A. Stamatoyannopoulos, Zibo Chen, 2020 .

Access the most recent version at doi: 10.1110/ps.03197403 References

Nick V Grishin, David Baker, Ruslan I Sadreyev, 2003 .

Crystal structures and increased stabilization of the protein G variants with switched folding pathways NuG1 and NuG2

David Baker, Brian Kuhlman, David Teller, 2002 .

Residues participating in the protein folding nucleus do not exhibit preferential evolutionary conservation.

Kevin W Plaxco, David Baker, Ingo Ruczinski, 2002, Journal of molecular biology.

ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility

Jens Meiler, David Baker, D. Baker, 2006, Proteins.

Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings

Oliver F. Lange, David Baker, Frank DiMaio, 2011, Journal of the American Chemical Society.

Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer

Michael J MacCoss, David Baker, Alex Zelter, 2016, eLife.

The effects of mutations on motions of side-chains in protein L studied by 2H NMR dynamics and scalar couplings.

David Baker, D. Baker, L. Kay, 2003, Journal of molecular biology.

A hybrid NMR/SAXS‐based approach for discriminating oligomeric protein interfaces using Rosetta

David Baker, Joseph R Luft, Edward H Snell, 2015, Proteins.

A model of anthrax toxin lethal factor bound to protective antigen.

David Baker, Ora Schueler-Furman, Kristina Cunningham, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Isotope signatures allow identification of chemically cross-linked peptides by mass spectrometry: a novel method to determine interresidue distances in protein structures through cross-linking.

Michael J MacCoss, David Baker, Alex Zelter, 2010, Journal of proteome research.

Ca2+ indicators based on computationally redesigned calmodulin-peptide pairs.

David Baker, Tanja Kortemme, Amy E Palmer, 2006, Chemistry & biology.

Building de novo cryo-electron microscopy structures collaboratively with citizen scientists

David Baker, Seth Cooper, Irina Gutsche, 2019, PLoS biology.

Cryo‐EM model validation using independent map reconstructions

David Baker, Wah Chiu, Frank DiMaio, 2013, Protein science : a publication of the Protein Society.

Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold.

David Baker, Lindsey Doyle, Nephi Stella, 2018, Protein engineering, design & selection : PEDS.

Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs

David Baker, Barry L. Stoddard, Justin Ashworth, 2010, Nucleic acids research.

An integrated device for the rapid and sensitive detection of the influenza hemagglutinin.

David Baker, Paul Yager, Joshua R. Buser, 2019, Lab on a chip.

Protein–protein docking predictions for the CAPRI experiment

David Baker, Tanja Kortemme, Jeffrey J. Gray, 2003, Proteins.

Massively parallel determination and modeling of endonuclease substrate specificity

David Baker, T. J. Brunette, Philip Bradley, 2014, Nucleic acids research.

Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples

Oliver F. Lange, David Baker, James M Aramini, 2012, Proceedings of the National Academy of Sciences.

Structure of the BamC two-domain protein obtained by Rosetta with a limited NMR data set.

Oliver F. Lange, David Baker, Oliver F Lange, 2011, Journal of molecular biology.

Prediction of the structure of symmetrical protein assemblies

David Baker, Philip Bradley, Ingemar André, 2007, Proceedings of the National Academy of Sciences.

Progress in AB Initio Protein Structure Prediction

David Baker, D. Baker, D. Baker, 2002, TheScientificWorldJournal.

Immobilizing affinity proteins to nitrocellulose: a toolbox for paper-based assay developers

David Baker, Paul Yager, Elain Fu, 2016, Analytical and Bioanalytical Chemistry.

The structure of a receptor with two associating transmembrane domains on the cell surface: integrin alphaIIbbeta3.

David Baker, Patrick Barth, Jieqing Zhu, 2009, Molecular cell.

Emergence of symmetry in homooligomeric biological assemblies

David Baker, Philip Bradley, Ingemar André, 2008, Proceedings of the National Academy of Sciences.

Improving 3D structure prediction from chemical shift data

Oliver F. Lange, David Baker, Yang Shen, 2013, Journal of biomolecular NMR.

Strand‐loop‐strand motifs: Prediction of hairpins and diverging turns in proteins

Jens Meiler, David Baker, Michael Kuhn, 2004, Proteins.

Computational design of novel protein binders and experimental affinity maturation.

David Baker, Sarel J Fleishman, Timothy A. Whitehead, 2013, Methods in enzymology.

Precise assembly of complex beta sheet topologies from de novo designed building blocks

David Baker, Gaetano T Montelione, Frank DiMaio, 2015, eLife.

Voltage sensor conformations in the open and closed states in ROSETTA structural models of K(+) channels.

David Baker, William A Catterall, Vladimir Yarov-Yarovoy, 2006, Proceedings of the National Academy of Sciences of the United States of America.