D. Baker

发表

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

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

A Potent Anti-Malarial Human Monoclonal Antibody Targets Circumsporozoite Protein Minor Repeats and Neutralizes Sporozoites in the Liver.

Jorgen W. Nelson, D. Baker, R. Gottardo, 2020, Immunity.

Relaxation of backbone bond geometry improves protein energy landscape modeling

D. Baker, F. Dimaio, M. Tyka, 2014, Protein science : a publication of the Protein Society.

High-resolution comparative modeling with RosettaCM.

David Baker, James Thompson, Frank DiMaio, 2013, Structure.

Improved protein structure prediction using predicted interresidue orientations

Jianyi Yang, David Baker, Ivan Anishchenko, 2019, Proceedings of the National Academy of Sciences.

Assigning function to yeast proteins by integration of technologies.

Brian E Snydsman, D. Baker, S. Fields, 2003, Molecular cell.

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.

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

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

Quadrivalent influenza nanoparticle vaccines induce broad protection

D. Baker, J. Mascola, D. Veesler, 2021, Nature.

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Brian D. Weitzner, Lars Malmström, Karen R. Khar, 2020, Nature Methods.

Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy

D. Baker, T. Yeates, I. André, 2012, Science.

Multivalent designed proteins protect against SARS-CoV-2 variants of concern

Wadim L. Matochko, Benjamin S. Freedman, D. Baker, 2021, bioRxiv.

Sentinel cells enable genetic detection of SARS-CoV-2 Spike protein

Zara Y. Weinberg, D. Baker, H. El-Samad, 2021, bioRxiv.

De novo design of modular and tunable protein biosensors

Robert A. Langan, D. Baker, S. Boyken, 2021, Nature.

Alternate states of proteins revealed by detailed energy landscape mapping.

D. Baker, F. Dimaio, M. Tyka, 2011, Journal of molecular biology.

Protein structure prediction and analysis using the Robetta server

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

Computational Alanine Scanning of Protein-Protein Interfaces

David E. Kim, D. Baker, T. Kortemme, 2004, Science's STKE.

A simple physical model for binding energy hot spots in protein–protein complexes

D. Baker, T. Kortemme, D. Baker, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Protein-protein docking with backbone flexibility.

Chu Wang, P. Bradley, D. Baker, 2007, Journal of Molecular Biology.

Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution.

D. Baker, B. Stoddard, B. Kuhlman, 2006, 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.

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.

Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens

D. Baker, P. Zwart, M. J. Bick, 2020, bioRxiv.

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

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

Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology

Richard Bonneau, D. Baker, C. Strauss, 2007, PLoS biology.

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions.

C Kooperberg, D Baker, K T Simons, 1997, Journal of molecular biology.

Assessment of predictions submitted for the CASP7 domain prediction category

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

Structure prediction for CASP7 targets using extensive all‐atom refinement with Rosetta@home

Lars Malmström, David Baker, Dylan Chivian, 2007, Proteins.

Control of repeat protein curvature by computational protein design

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

De novo protein design by deep network hallucination

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

Atomic accuracy in predicting and designing noncanonical RNA structure

J. Karanicolas, Rhiju Das, D. Baker, 2010, Nature Methods.

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

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

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

D. Baker, Hetunandan Kamisetty, S. Ovchinnikov, 2014, eLife.

The Rosetta all-atom energy function for macromolecular modeling and design

Roland L. Dunbrack, Jason W. Labonte, Jeffrey J. Gray, 2017, bioRxiv.

Rosetta in CAPRI rounds 13–19

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

Scientific benchmarks for guiding macromolecular energy function improvement.

Jack Snoeyink, Yifan Song, James Thompson, 2013, Methods in enzymology.

Remodeling a β-peptide bundle

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

Macromolecular modeling with rosetta.

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

Automated de novo prediction of native-like RNA tertiary structures

D. Baker, Rhiju Das, D. Baker, 2007, Proceedings of the National Academy of Sciences.

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

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

Protein Structure Prediction Using Rosetta

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

Contact order, transition state placement and the refolding rates of single domain proteins.

D. Baker, K. Simons, K. Plaxco, 1998, Journal of molecular biology.

Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease

D. Baker, M. Diamond, Inna Goreshnik, 2021, Cell Host & Microbe.

Ultrapotent miniproteins targeting the receptor-binding domain protect against SARS-CoV-2 infection and disease in mice

D. Baker, M. Diamond, Inna Goreshnik, 2021, bioRxiv.

Structural and energetic basis of folded protein transport by the FimD usher

D. Baker, G. Waksman, S. Hultgren, 2013, Nature.

Computational Design of High-Affinity Epitope Scaffolds by Backbone Grafting of a Linear Epitope

D. Baker, E. Pai, Y. Ban, 2011, Journal of Molecular Biology.

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

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

RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

D. Baker, I. André, Po-Ssu Huang, 2011, PloS one.

Incorporation of evolutionary information into Rosetta comparative modeling

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

Modeling Symmetric Macromolecular Structures in Rosetta3

David Baker, Andrew Leaver-Fay, Frank DiMaio, 2011, PloS one.

Structure-guided forcefield optimization

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

Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs

David Baker, Barry L. Stoddard, Justin Ashworth, 2010, 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.

RosettaLigand docking with full ligand and receptor flexibility.

Ian W. Davis, K. Shadan, E. Rodriguez, 2009, Journal of molecular biology.

Redesigning the specificity of protein-DNA interactions with Rosetta.

Summer B. Thyme, D. Baker, D. Baker, 2014, Methods in molecular biology.

Direction of actin flow dictates integrin LFA-1 orientation during leukocyte migration

Shalin B. Mehta, Talley J. Lambert, D. Baker, 2017, bioRxiv.

The utility of early end-tidal capnography in monitoring ventilation status after severe injury.

D. Baker, M. Copass, E. Bulger, 2009, Journal of Trauma.

GTP-binding Ypt1 protein and Ca2+ function independently in a cell-free protein transport reaction.

D. Baker, D. Botstein, R. Schekman, 1990, Proceedings of the National Academy of Sciences of the United States of America.

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

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

Quantitative reactivity profiling predicts functional cysteines in proteomes

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

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.

Engineering an allosteric transcription factor to respond to new ligands

Farren J. Isaacs, Alexander S. Garruss, Alexander S Garruss, 2015, Nature Methods.

Self-assembly–based posttranslational protein oscillators

D. Baker, M. Brenner, Ofer Kimchi, 2020, Science advances.

Self-assembly–based posttranslational protein oscillators

D. Baker, M. Brenner, Ofer Kimchi, 2020, bioRxiv.

Ab initio protein structure prediction: progress and prospects.

Richard Bonneau, D. Baker, D. Baker, 2001, Annual review of biophysics and biomolecular structure.

Next-Generation Surrogate Wnts Support Organoid Growth and Deconvolute Frizzled Pleiotropy In Vivo.

Luke T. Dang, D. Baker, K. Garcia, 2020, Cell stem cell.

Surrogate Wnt agonists that phenocopy canonical Wnt/β-catenin signaling

Luke T. Dang, D. Baker, K. Garcia, 2017, Nature.

Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition.

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

Exploring the repeat protein universe through computational protein design

David Baker, John A. Tainer, Po-Ssu Huang, 2015, Nature.

A general computational approach for repeat protein design.

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

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

P. Bradley, D. Baker, B. Stoddard, 2015 .

Progress in Modeling of Protein Structures and Interactions

O. Schueler‐Furman, Chu Wang, P. Bradley, 2005, Science.

Reconfigurable asymmetric protein assemblies through implicit negative design

D. Baker, Y. Hsia, F. Praetorius, 2021, bioRxiv.

Design of multi-scale protein complexes by hierarchical building block fusion

D. Baker, M. J. Bick, D. Veesler, 2021, Nature Communications.

Improved protein structure refinement guided by deep learning based accuracy estimation

Minkyung Baek, Naozumi Hiranuma, Hahnbeom Park, 2020, Nature Communications.

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

D. Baker, B. Coventry, D. Baker, 2020, bioRxiv.

Modular repeat protein sculpting using rigid helical junctions

D. Baker, M. J. Bick, T. Brunette, 2020, 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.

Topological control of cytokine receptor signaling induces differential effects in hematopoiesis

D. Baker, K. Garcia, G. Ueda, 2019, Science.

Programmable design of orthogonal protein heterodimers

Robert A. Langan, Zachary L. VanAernum, D. Baker, 2018, Nature.

Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design.

Brian Kuhlman, David Baker, Jack B. Maguire, 2018, Journal of chemical theory and computation.

Global analysis of protein folding using massively parallel design, synthesis, and testing

D. Baker, Alex Ford, V. Mulligan, 2017, Science.

Computational Design of Self-Assembling Cyclic Protein Homo-oligomers

J. H. Pereira, D. Baker, P. Zwart, 2016, Nature chemistry.

CASP11 refinement experiments with ROSETTA

Frank DiMaio, Hahnbeom Park, David Baker, 2016, Proteins.

Protein interaction networks revealed by proteome coevolution

D. Baker, Q. Cong, S. Ovchinnikov, 2019, Science.

Surrogate Wnt agonists that phenocopy canonical Wnt and β-catenin signalling

Hans Clevers, Junlei Chang, Claudia y. Janda, 2017, Nat..

Computational design of ligand-binding proteins with high affinity and selectivity

David Baker, Barry L. Stoddard, Sagar D. Khare, 2013, Nature.

High Resolution Mapping of Protein Sequence–Function Relationships

D. Baker, S. Fields, S. Fleishman, 2010, Nature Methods.

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.

Computational design of a protein-based enzyme inhibitor.

D. Baker, G. Montelione, S. Fleishman, 2013, Journal of molecular biology.

De novo design of a fluorescence-activating β-barrel

William Sheffler, Binchen Mao, Barry L. Stoddard, 2018, Nature.

The 3D profile method for identifying fibril-forming segments of proteins.

D. Baker, D. Eisenberg, M. Thompson, 2006, Proceedings of the National Academy of Sciences of the United States of America.

VaxCelerate II: Rapid development of a self-assembling vaccine for Lassa fever

D. Baker, A. D. De Groot, H. S. Warren, 2014, Human vaccines & immunotherapeutics.

Chain collapse can occur concomitantly with the rate-limiting step in protein folding

D. Baker, K. Plaxco, I. Millett, 1999, Nature Structural Biology.

A protein-folding reaction under kinetic control

D. Baker, D. Agard, J. Sohl, 1992, Nature.

Recurring local sequence motifs in proteins.

D. Baker, K. F. Han, D. Baker, 1995, Journal of molecular biology.

Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta

David E. Kim, D. Baker, F. Dimaio, 2016, Proteins.

Structurally Mapping Endogenous Heme in the CcmCDE Membrane Complex for Cytochrome c Biogenesis.

D. Baker, S. Ovchinnikov, Molly C. Sutherland, 2018, Journal of molecular biology.

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.

Toward High-Resolution de Novo Structure Prediction for Small Proteins

P. Bradley, K. Misura, D. Baker, 2005, Science.

Discovery and engineering of enhanced SUMO protease enzymes

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

Cryo‐EM model validation using independent map reconstructions

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

De novo design of self-assembling helical protein filaments

D. Baker, G. Oberdorfer, W. Sheffler, 2018, Science.

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

David Baker, Andrew Leaver-Fay, Seth Cooper, 2017, Bioinform..

What has de novo protein design taught us about protein folding and biophysics?

David Baker, D. Baker, D. Baker, 2019, Protein science : a publication of the Protein Society.

Protein sequence design by conformational landscape optimization

David E. Kim, D. Baker, S. Ovchinnikov, 2021, Proceedings of the National Academy of Sciences.

Design of proteins presenting discontinuous functional sites using deep learning

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

Ab initio protein structure prediction of CASP III targets using ROSETTA

Richard Bonneau, D. Baker, I. Ruczinski, 1999, Proteins.

Emergence of symmetry in homooligomeric biological assemblies

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

Predicting protein structures with a multiplayer online game

Adrien Treuille, Andrew Leaver-Fay, David Baker, 2010, Nature.

Mammalian display screening of diverse cystine-dense peptides for difficult to drug targets

P. Bradley, D. Baker, J. Olson, 2017, Nature Communications.

Large-scale design and refinement of stable proteins using sequence-only models

Craig O. Mackenzie, D. Baker, Alex Ford, 2021, bioRxiv.

RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design, and validation

D. Baker, W. Sheffler, D. Baker, 2008, Protein science : a publication of the Protein Society.

The coming of age of de novo protein design

D. Baker, S. Boyken, Po-Ssu Huang, 2016, Nature.

ProteinGCN: Protein model quality assessment using Graph Convolutional Networks

David Baker, Ivan Anishchenko, Partha Talukdar, 2020, bioRxiv.

Airway Management in Emergencies.

D. Baker, 2009 .

CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge

Richard D. Smith, Heather A. Carlson, David Baker, 2016, J. Chem. Inf. Model..

Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.

Jeffrey J. Gray, Stewart E. Moughon, O. Schueler‐Furman, 2003, Journal of molecular biology.

Enantioselective enzymes by computational design and in silico screening.

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

An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes.

D. Baker, A. Morozov, T. Kortemme, 2003, Journal of molecular biology.

Protein-protein docking with backbone flexibility.

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

CASP6 assessment of contact prediction

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

The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice

D. Baker, D. Agard, J. Bondy-Denomy, 2022, bioRxiv.

Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008

Charles L. Brooks, Adrian W. R. Serohijos, John Moult, 2009, Nature Reviews Drug Discovery.

Automated prediction of CASP‐5 structures using the Robetta server

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

Prediction and structural characterization of an independently folding substructure in the src SH3 domain.

D Baker, D. Baker, C. Bystroff, 1998, Journal of molecular biology.

Trapping a transition state in a computationally designed protein bottle

D. Baker, P. Schultz, R. Stevens, 2015, Science.

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.

Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction

Jasmine L. Gallaher, D. Baker, J. Siegel, 2010, Science.

Algorithm discovery by protein folding game players

David Baker, Zoran Popovic, Kefan Xu, 2011, Proceedings of the National Academy of Sciences.

Realistic protein–protein association rates from a simple diffusional model neglecting long‐range interactions, free energy barriers, and landscape ruggedness

D. Baker, M. Schlosshauer, D. Baker, 2004, Protein science : a publication of the Protein Society.

Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites

Brian D. Weitzner, Timothy W. Craven, Stephen A. Rettie, 2021, Nature Communications.

Report of the National Institutes of Health SARS-CoV-2 Antiviral Therapeutics Summit

Mindy I. Davis, D. Baker, D. Hazuda, 2021, The Journal of infectious diseases.

Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules.

David E. Kim, P. Bradley, D. Baker, 2016, Journal of chemical theory and computation.

Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design

D. Baker, R. Samudrala, Gong Cheng, 2005, Nucleic acids research.

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 .

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.

Consistent blind protein structure generation from NMR chemical shift data

Oliver F. Lange, D. Baker, Gaohua Liu, 2008, Proceedings of the National Academy of Sciences.

Structural inference of native and partially folded RNA by high-throughput contact mapping

Magdalena A. Jonikas, D. Baker, R. Altman, 2008, Proceedings of the National Academy of Sciences.

Enhancing and shaping the immunogenicity of native-like HIV-1 envelope trimers with a two-component protein nanoparticle

D. Baker, J. Bale, John P. Moore, 2019, Nature Communications.

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.

The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction

D. Baker, S. Fleishman, Nicola A. G. Meenan, 2010, Proceedings of the National Academy of Sciences.

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

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

Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts

D. Baker, J. Kelly, D. Ekiert, 2014, 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.

Computer Designed PRC2 Inhibitor, EBdCas9, Reveals Functional TATA boxes in Distal Promoter Regions

D. Baker, H. Ruohola-Baker, R. D. Hawkins, 2020, bioRxiv.

Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein-Ligand Docking.

D. Baker, Hahnbeom Park, Guangfeng Zhou, 2021, Journal of chemical theory and computation.

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.

Engineering of Kuma030: A Gliadin Peptidase That Rapidly Degrades Immunogenic Gliadin Peptides in Gastric Conditions.

D. Baker, G. Montelione, J. Siegel, 2015, Journal of the American Chemical Society.

Removing T-cell epitopes with computational protein design

David Baker, Chris King, Marion Pepper, 2014, Proceedings of the National Academy of Sciences.

Heterologous Epitope-Scaffold Prime∶Boosting Immuno-Focuses B Cell Responses to the HIV-1 gp41 2F5 Neutralization Determinant

D. Baker, R. Wyatt, W. Schief, 2011, PloS one.

High‐accuracy refinement using Rosetta in CASP13

Gyu Rie Lee, Hahnbeom Park, Ivan Anishchanka, 2019, Proteins.

Protein structure prediction using Rosetta in CASP12

Frank DiMaio, Hahnbeom Park, David Baker, 2018, Proteins.

RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite

Jens Meiler, Florian Richter, Sarel J. Fleishman, 2011, PloS one.

Improved recognition of native‐like protein structures using a combination of sequence‐dependent and sequence‐independent features of proteins

D. Baker, C. Kooperberg, I. Ruczinski, 1999, Proteins.

Detection of antibodies neutralizing historical and emerging SARS-CoV-2 strains using a thermodynamically coupled de novo biosensor system

D. Baker, M. Diamond, A. Walls, 2021, bioRxiv.

Atomic model of the type III secretion system needle

D. Baker, S. Becker, C. Griesinger, 2012, Nature.

Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation

Jason T. Stevens, D. Baker, D. Eisenberg, 2011, Nature.

Cooperative hydrogen bonding in amyloid formation

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

Generation of ordered protein assemblies using rigid three-body fusion

Robert A. Langan, D. Baker, G. Jensen, 2020, Proceedings of the National Academy of Sciences.

Matching theory and experiment in protein folding.

D. Baker, E. Alm, D. Baker, 1999, Current opinion in structural biology.

Comprehensive computational design of ordered peptide macrocycles

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

Simultaneous prediction of protein folding and docking at high resolution

D. Baker, I. André, Rhiju Das, 2009, Proceedings of the National Academy of Sciences.

Polyclonal antibody responses to HIV Env immunogens resolved using cryoEM

D. Baker, John P. Moore, D. Burton, 2021, Nature Communications.

Designed proteins assemble antibodies into modular nanocages

D. Baker, L. Stamatatos, H. Ruohola-Baker, 2021, Science.

Designed proteins assemble antibodies into modular nanocages

D. Baker, L. Stamatatos, H. Ruohola-Baker, 2020, bioRxiv.

Searching for folded proteins in vitro and in silico.

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

Elicitation of broadly protective immunity to influenza by multivalent hemagglutinin nanoparticle vaccines

D. Baker, J. Mascola, D. Veesler, 2020, bioRxiv.

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

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

De novo design of picomolar SARS-CoV-2 miniprotein inhibitors

D. Baker, M. Diamond, A. Walls, 2020, Science.

Parallelized identification of on- and off-target protein interactions.

David Baker, Jiayi Dou, Inna Goreshnik, 2020, Molecular systems design & engineering.

Functional expression and characterization of the envelope glycoprotein E1E2 heterodimer of hepatitis C virus

D. Baker, Q. Cong, Zibo Chen, 2019, PLoS pathogens.

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.

Origins of catalysis by computationally designed retroaldolase enzymes

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

Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase

D. Baker, D. Hilvert, P. Mittl, 2016, Nature Chemistry.

Active Site Plasticity of a Computationally Designed Retro‐Aldolase Enzyme

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

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

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

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.

Kemp elimination catalysts by computational enzyme design

Eric A. Althoff, Dan S. Tawfik, Jasmine L. Gallaher, 2008, Nature.

De Novo Computational Design of Retro-Aldol Enzymes

Eric A. Althoff, Jasmine L. Gallaher, D. Baker, 2008, Science.

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.

Blind docking of pharmaceutically relevant compounds using RosettaLigand

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

A Pareto-Optimal Refinement Method for Protein Design Scaffolds

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

Protein Nanocontainers from Nonviral Origin: Testing the Mechanics of Artificial and Natural Protein Cages by AFM.

D. Baker, W. Roos, G. Wuite, 2016, The journal of physical chemistry. B.

Incorporation of sensing modalities into de novo designed fluorescence-activating proteins

Rommie E. Amaro, Emília P. Barros, Min Yen Lee, 2021, Nature Communications.

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

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

Hierarchy of structure loss in MD simulations of src SH3 domain unfolding.

M Levitt, D Baker, M. Levitt, 1999, Journal of molecular biology.

Refinement of protein structures into low-resolution density maps using rosetta.

M. Baker, W. Chiu, M. Tyka, 2009 .

A general strategy to construct small molecule biosensors in eukaryotes

Mauricio S. Antunes, D. Baker, G. Church, 2015, eLife.

Multipass membrane protein structure prediction using Rosetta

D. Baker, V. Yarov-Yarovoy, J. Schonbrun, 2005, Proteins.

Atomic accuracy models from 4.5 Å cryo-electron microscopy data with density-guided iterative local refinement

Matthias J. Brunner, D. Baker, F. Dimaio, 2015, Nature Methods.

The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy.

D. Baker, J. Meiler, D. Baker, 2005, Journal of magnetic resonance.

Rapid protein fold determination using unassigned NMR data

D. Baker, J. Meiler, D. Baker, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Coupled prediction of protein secondary and tertiary structure

D. Baker, J. Meiler, D. Baker, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Contact order and ab initio protein structure prediction

Richard Bonneau, D. Baker, J. Tsai, 2002, Protein science : a publication of the Protein Society.

De novo determination of protein backbone structure from residual dipolar couplings using Rosetta.

D. Baker, C. Rohl, D. Baker, 2002, Journal of the American Chemical Society.

De novo protein structure determination using sparse NMR data

D. Baker, C. Strauss, P. Bowers, 2000, Journal of biomolecular NMR.

Insights from the crystal structure of the sixth BRCT domain of topoisomerase IIβ binding protein 1

D. Baker, E. Kellogg, J. Glover, 2009, Protein science : a publication of the Protein Society.

Deep learning enables the atomic structure determination of the Fanconi Anemia core complex from cryoEM

D. Baker, F. Dimaio, I. Anishchenko, 2020, bioRxiv.

Targeting HIV Env immunogens to B cell follicles in nonhuman primates through immune complex or protein nanoparticle formulations

D. Baker, D. Irvine, N. King, 2020, npj Vaccines.

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

Dongsheng Li, Huayou Su, Frank DiMaio, 2017, Nature.

High-Resolution Microtubule Structures Reveal the Structural Transitions in αβ-Tubulin upon GTP Hydrolysis

D. Baker, E. Nogales, G. Lander, 2014, Cell.

One contact for every twelve residues allows robust and accurate topology‐level protein structure modeling

David E. Kim, D. Baker, F. Dimaio, 2014, Proteins.

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.

A Refined Model of the Prototypical Salmonella SPI-1 T3SS Basal Body Reveals the Molecular Basis for Its Assembly

Samuel I. Miller, D. Baker, R. Pfuetzner, 2013, PLoS pathogens.

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..

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

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

phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta

Randy J. Read, Paul D. Adams, Nathaniel Echols, 2012, Journal of Structural and Functional Genomics.

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

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

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

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

First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor

Luke T. Dang, D. Baker, S. Orkin, 2017, Proceedings of the National Academy of Sciences.

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

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

Computational design of protein-protein interactions.

Tanja Kortemme, David Baker, D. Baker, 2004, Current opinion in chemical biology.

A surprising simplicity to protein folding

D. Baker, D. Baker, D. Baker, 2000, Nature.

Dissecting muscle and neuronal disorders in a Drosophila model of muscular dystrophy

A. S. Yatsenko, D. Baker, H. Ruohola-Baker, 2007, The EMBO journal.

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.

Engineering Biomolecular Self‐Assembly at Solid–Liquid Interfaces

D. Baker, Jiajun Chen, Shuai Zhang, 2020, Advances in Materials.

Ion-dependent protein–surface interactions from intrinsic solvent response

D. Baker, F. Tezcan, J. Pfaendtner, 2021, Proceedings of the National Academy of Sciences.

Controlling protein assembly on inorganic crystals through designed protein interfaces

D. Baker, Shuai Zhang, J. D. De Yoreo, 2019, Nature.

Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces

D. Baker, F. Dimaio, T. Gonen, 2015, Science.

De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy

D. Baker, Po-Ssu Huang, K. Feldmeier, 2015, Nature chemical biology.

Control over overall shape and size in de novo designed proteins

D. Baker, Gaohua Liu, G. Montelione, 2015, Proceedings of the National Academy of Sciences.

Principles for designing ideal protein structures

D. Baker, Gaohua Liu, G. Montelione, 2012, Nature.

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

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

Design of a hyperstable 60-subunit protein icosahedron

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

Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold

D. Baker, Po-Ssu Huang, Y. Ban, 2011, Science.

Elicitation of structure-specific antibodies by epitope scaffolds

D. Baker, R. Wyatt, W. Schief, 2010, Proceedings of the National Academy of Sciences.

Circularization changes the folding transition state of the src SH3 domain.

D Baker, D. Baker, V. Grantcharova, 2001, Journal of molecular biology.

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

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

Functional rapidly folding proteins from simplified amino acid sequences

D. Baker, Q. Yi, D. Riddle, 1997, Nature Structural Biology.

Massively parallel de novo protein design for targeted therapeutics

Lu Zhang, Xuhui Huang, David Baker, 2017, Nature.

Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design.

Summer B. Thyme, P. Bradley, D. Baker, 2012, Journal of molecular biology.

Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution.

David Baker, Orly Dym, Andrew M Wollacott, 2011, Journal of molecular biology.

Role of conformational sampling in computing mutation‐induced changes in protein structure and stability

D. Baker, A. Leaver-Fay, E. Kellogg, 2011, Proteins.

Motif‐directed flexible backbone design of functional interactions

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

Computational redesign of protein-protein interaction specificity

D. Baker, B. Stoddard, T. Kortemme, 2004, Nature Structural &Molecular Biology.

A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins.

D. Baker, B. Kuhlman, G. Dantas, 2003, Journal of molecular biology.

Computational redesign of endonuclease DNA binding and cleavage specificity

Ashworth, B. Stoddard, R. Monnat, 2006 .

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

Jason W. Labonte, Jeffrey J. Gray, Johanna K. S. Tiemann, 2021, Nature Communications.

Perturbing the energy landscape for improved packing during computational protein design

Jack B. Maguire, Samer F. Halabiya, Jermel R. Griffin, 2020, Proteins.

De novo design of tunable, pH-driven conformational changes

D. Baker, J. Lippincott-Schwartz, M. J. Bick, 2019, 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.

High thermodynamic stability of parametrically designed helical bundles

D. Baker, F. Dimaio, G. Oberdorfer, 2014, Science.

De novo design of protein logic gates

Michael C. Jewett, Galen Dods, Hana El-Samad, 2020, Science.

Modular and tunable biological feedback control using a de novo protein switch

David Baker, Mariana Gómez-Schiavon, Galen Dods, 2019, Nature.

De Novo Design of Bioactive Protein Switches

Vikram Khipple Mulligan, David Baker, Galen Dods, 2019, Nature.

Mechanisms of protein folding.

D Baker, D. Baker, E. Alm, 2001, Current opinion in structural biology.

O-GlcNAc modification of small heat shock proteins enhances their anti-amyloid chaperone activity

Paul M. Levine, Timothy W. Craven, D. Baker, 2021, Nature Chemistry.

Progress in protein–protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side‐chain flexibility

O. Schueler‐Furman, Chu Wang, D. Baker, 2005, Proteins.

Assessing the utility of coevolution-based residue–residue contact predictions in a sequence- and structure-rich era

D. Baker, Hetunandan Kamisetty, S. Ovchinnikov, 2013, Proceedings of the National Academy of Sciences.

Multiplex pairwise assembly of array-derived DNA oligonucleotides

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

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.

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.

Conversion of monomeric protein L to an obligate dimer by computational protein design

Kam Y. J. Zhang, D Baker, David E. Kim, 2001, Proceedings of the National Academy of Sciences of the United States of America.

Increased Diels-Alderase Activity through Foldit Player Guided Backbone Remodeling

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

An α-Helical Burst in the src SH3 Folding Pathway

D. Baker, H. Kihara, Yoshitaka Matsumura, 2007 .

An R-Helical Burst in the src SH 3 Folding Pathway

D. Baker, H. Kihara, Yoshitaka Matsumura, 2006 .

Critical role of β-hairpin formation in protein G folding

D. Baker, E. Alm, E. McCallister, 2000, Nature Structural Biology.

De novo design of modular and tunable allosteric biosensors

Scott E. Boyken, David Baker, Robert A. Langan, 2020, bioRxiv.

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

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

An enumerative algorithm for de novo design of proteins with diverse pocket structures

D. Baker, M. J. Bick, Inna Goreshnik, 2020, Proceedings of the National Academy of Sciences.

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

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

The structure, dynamics, and energetics of protein adsorption—lessons learned from adsorption of statherin to hydroxyapatite

J. R. Long, O. Schueler‐Furman, D. Baker, 2007, Magnetic resonance in chemistry : MRC.

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.

The modular structure of the inner-membrane ring component PrgK facilitates assembly of the type III secretion system basal body.

D. Baker, L. McIntosh, N. Sgourakis, 2015, 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.

Secretion System Serovar Typhimurium Type III Salmonella enterica of the Interactions of the Transmembrane Polymeric Rings 2010

D. Baker, R. Pfuetzner, I. André, 2010 .

High-resolution structure prediction and the crystallographic phase problem

P. Bradley, D. Baker, B. Qian, 2007, Nature.

Prediction of the structure of symmetrical protein assemblies

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

Improving the Efficiency of Ligand-Binding Protein Design with Molecular Dynamics.

Rommie E. Amaro, David Baker, Rommie E Amaro, 2019, Journal of chemical theory and computation.

Computational design of environmental sensors for the potent opioid fentanyl

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

Evolution of a designed protein assembly encapsulating its own RNA genome

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

Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta.

Matthew J. O’Meara, P. Bradley, D. Baker, 2015, Journal of chemical theory and computation.

Self-Assembling 2D Arrays with de Novo Protein Building Blocks.

D. Baker, M. J. Bick, S. Boyken, 2019, Journal of the American Chemical Society.

Designed protein logic to target cells with precise combinations of surface antigens

Robert A. Langan, Garreck H. Lenz, D. Baker, 2020, Science.

Evaluation and optimization of discrete state models of protein folding.

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

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.

Intratumoral activation of the necroptotic pathway components RIPK1 and RIPK3 potentiates antitumor immunity

D. Baker, A. Oberst, B. Daniels, 2019, Science Immunology.

Computational Protein Design for Synthetic Biology

D. Baker, Florian Richter, D. Baker, 2013 .

Simplified proteins: minimalist solutions to the 'protein folding problem'.

D Baker, D. Baker, D. Riddle, 1998, Current opinion in structural biology.

Prediction of membrane protein structures with complex topologies using limited constraints

D Baker, D. Baker, P. Barth, 2009, Proceedings of the National Academy of Sciences.

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

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

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.

A covariation analysis reveals elements of selectivity in quorum sensing systems

D. Baker, Q. Cong, E. Greenberg, 2021, bioRxiv.

Template Scoring Methods for Protein Torsion Angle Prediction

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

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.

An alpha-helical burst in the src SH3 folding pathway.

D. Baker, H. Kihara, Yoshitaka Matsumura, 2007, Biochemistry.

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.

A Vast Repertoire of Dscam Binding Specificities Arises from Modular Interactions of Variable Ig Domains

D. Baker, B. Qian, S. Zipursky, 2007, Cell.

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

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

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

Z. Popovic, D. Baker, Firas Khatib, 2011, Nature Structural &Molecular Biology.

Structure prediction for CASP8 with all‐atom refinement using Rosetta

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

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.

A breakdown of symmetry in the folding transition state of protein L.

D Baker, D. Baker, D. Kim, 2000, Journal of molecular biology.

Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures.

E. Alm, D. Baker, D. Baker, 1999, Proceedings of the National Academy of Sciences of the United States of America.

APOBEC2 is a monomer in solution: implications for APOBEC3G models.

Troy C. Krzysiak, D. Baker, James M Thompson, 2012, Biochemistry.

De Novo Enzyme Design Using Rosetta3

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

Accurate prediction of protein structures and interactions using a 3-track neural network

Gyu Rie Lee, J. H. Pereira, D. Baker, 2021, Science.

Actin retrograde flow actively aligns and orients ligand-engaged integrins in focal adhesions

Shalin B. Mehta, D. Baker, S. Mayor, 2016, Proceedings of the National Academy of Sciences.

Modulation of Integrin Activation by an Entropic Spring in the β-Knee*

D. Baker, Po-Ssu Huang, T. Springer, 2010, Journal of Biological Chemistry.

Reconstitution of SEC gene product-dependent intercompartmental protein transport

D. Baker, R. Schekman, M. Rexach, 1988, Cell.

Accurate design of co-assembling multi-component protein nanomaterials

David Baker, Neil P. King, William Sheffler, 2014, Nature.

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.

De novo protein structure generation from incomplete chemical shift assignments

A. Bax, R. Vernon, Yang Shen, 2009, Journal of biomolecular NMR.

Design of Biologically Active Binary Protein 2D Materials

Ariel J. Ben-Sasson, D. Baker, H. Ruohola-Baker, 2020, Nature.

Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion

D. Baker, M. J. Bick, D. Hilvert, 2020, Proceedings of the National Academy of Sciences.

Computational design of closely related proteins that adopt two well-defined but structurally divergent folds

D. Baker, M. J. Bick, D. Fletcher, 2020, Proceedings of the National Academy of Sciences.

Forced Protein Unfolding Leads to Highly Elastic and Tough Protein Hydrogels

D. Baker, M. Rief, N. Koga, 2013, Nature Communications.

Complementary Chimeric Isoforms Reveal Dscam1 Binding Specificity In Vivo

D. Heeger, D. Baker, S. Zipursky, 2012, Neuron.

Interpreting neural networks for biological sequences by learning stochastic masks

Alyssa La Fleur, D. Baker, Sreeram Kannan, 2021, Nature Machine Intelligence.

Comparative analysis of mutant tyrosine kinase chemical rescue.

D. Baker, J. Kuriyan, J. Havranek, 2009, Biochemistry.

De novo Design of a Highly Specific Inhibitor of Integrin Αvβ6 for Pulmonary Fibrosis

Dean A. Slocum, G. Raghu, J. Cochran, 2021 .

Sampling bottlenecks in de novo protein structure prediction.

David E. Kim, P. Bradley, D. Baker, 2009, Journal of molecular biology.

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.

Receptor subtype discrimination using extensive shape complementary designed interfaces

Luke T. Dang, K. Garcia, Keunwan Park, 2019, Nature Structural & Molecular Biology.

Comprehensive computational design of mCreI homing endonuclease cleavage specificity for genome engineering

Umut Y. Ulge, D. Baker, R. Monnat, 2011, Nucleic acids research.

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

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

A desolvation barrier to hydrophobic cluster formation may contribute to the rate‐limiting step in protein folding

D Baker, D. Baker, J A Rank, 1997, Protein science : a publication of the Protein Society.

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

Timothy A. Whitehead, D. Baker, I. Wilson, 2011, Science.

A computationally engineered RAS rheostat reveals RAS/ERK signaling dynamics

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