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List of works by David Baker

A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces

scientific article published in March 2005

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

scientific article

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

scientific article

A De Novo Protein Binding Pair By Computational Design and Directed Evolution

scientific article

A Double S Shape Provides the Structural Basis for the Extraordinary Binding Specificity of Dscam Isoforms

scientific article

A General Expression for Bimolecular Association Rates with Orientational Constraints

article

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

scientific article

A Pareto-optimal refinement method for protein design scaffolds

scientific article

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

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

scientific article published in Nature Communications

A computational method for design of connected catalytic networks in proteins

scientific article published on 01 December 2019

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

scientific article

A general computational approach for repeat protein design

scientific article

A general strategy to construct small molecule biosensors in eukaryotes

scientific article published on 29 December 2015

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

scientific article published on 19 December 2014

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

scientific article

A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys

scientific article (publication date: 2004)

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

scientific article published in April 2009

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

scientific article published on June 1995

A protein-folding reaction under kinetic control

scientific article published in March 1992

A putative Src homology 3 domain binding motif but not the C-terminal dystrophin WW domain binding motif is required for dystroglycan function in cellular polarity in Drosophila

scientific article

A refined model of the prototypical Salmonella SPI-1 T3SS basal body reveals the molecular basis for its assembly

scientific article (publication date: 2013)

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

scientific article (publication date: 29 October 2002)

A simple physical model for the prediction and design of protein-DNA interactions

scientific article

A synthetic homing endonuclease-based gene drive system in the human malaria mosquito

scientific article

A vast repertoire of Dscam binding specificities arises from modular interactions of variable Ig domains.

scientific article

APOBEC2 is a monomer in solution: implications for APOBEC3G models

scientific article published on 27 February 2012

Accurate automated protein NMR structure determination using unassigned NOESY data

scientific article

Accurate computational design of multipass transmembrane proteins.

scientific article published in March 2018

Accurate computer-based design of a new backbone conformation in the second turn of protein L

scientific article

Accurate de novo design of hyperstable constrained peptides

scientific article

Accurate design of co-assembling multi-component protein nanomaterials

scientific article

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

scientific article

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

scientific article

Accurate protein structure modeling using sparse NMR data and homologous structure information

scientific article

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

scientific article published on 28 February 2013

Algorithm discovery by protein folding game players

scientific article

Alteration of enzyme specificity by computational loop remodeling and design

scientific article

Alternate states of proteins revealed by detailed energy landscape mapping

scientific article

Amyloid β peptide cleavage by kallikrein 7 attenuates fibril growth and rescues neurons from Aβ-mediated toxicity in vitro

scientific article

An alpha-helical burst in the src SH3 folding pathway

scientific article

An engineered microbial platform for direct biofuel production from brown macroalgae.

scientific article

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

scientific article published on 24 August 2020

An exciting but challenging road ahead for computational enzyme design

scientific article

An improved protein decoy set for testing energy functions for protein structure prediction.

scientific article

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

scientific article

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

scientific article

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

scientific article (publication date: 25 April 1997)

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

scientific article

Assessment of predictions submitted for the CASP7 domain prediction category.

scientific article

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

scientific article published on 23 April 2009

Assigning function to yeast proteins by integration of technologies.

scientific article

Atomic accuracy in predicting and designing noncanonical RNA structure

scientific article

Atomic model of the type III secretion system needle

scientific article

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

scientific article

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

scholarly article published in Nature Communications

Automated de novo prediction of native-like RNA tertiary structures

scientific article

Automated prediction of CASP-5 structures using the Robetta server.

scientific article

Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM.

scientific article

Automating human intuition for protein design

scientific article published on 22 November 2013

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

scientific article published on 08 June 2014

Blind docking of pharmaceutically relevant compounds using RosettaLigand

scientific article published on September 2009

Blind testing of routine, fully automated determination of protein structures from NMR data

scientific article

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

scientific article

CASD-NMR: critical assessment of automated structure determination by NMR

scientific article

CASP6 assessment of contact prediction.

scientific article

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

scientific article published on 9 October 2015

Ca2+ indicators based on computationally redesigned calmodulin-peptide pairs

scientific article published in May 2006

Catalytic efficiencies of directly evolved phosphotriesterase variants with structurally different organophosphorus compounds in vitro

scientific article published on 26 November 2015

Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination

scientific article

Centenary Award and Sir Frederick Gowland Hopkins Memorial Lecture. Protein folding, structure prediction and design.

scientific article

Chapter 7 Reconstitution of Protein Transport Using Broken Yeast Spheroplasts

article by David Baker & Randy Schekman published 1989 in Methods in Cell Biology

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

scientific article

Characterization of the free energy spectrum of peptostreptococcal protein L

scientific article published on 01 January 1997

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

scientific article

Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations

scientific article (publication date: 4 May 2004)

Clustering of low-energy conformations near the native structures of small proteins

scientific article

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

scientific article (publication date: 10 February 2015)

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

scientific article

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

scientific article

Comparative Analysis of Mutant Tyrosine Kinase Chemical Rescue † ‡

scientific article

Comparison of Quantum Mechanics and Molecular Mechanics Dimerization Energy Landscapes for Pairs of Ring-Containing Amino Acids in Proteins

scholarly article by Alexandre V. Morozov et al published June 2004 in Journal of Physical Chemistry

Comparison of designed and randomly generated catalysts for simple chemical reactions

scientific article

Complementary Chimeric Isoforms Reveal Dscam1 Binding Specificity In Vivo

Complementary chimeric isoforms reveal Dscam1 binding specificity in vivo

scientific article published on April 2012

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

scientific article

Comprehensive computational design of ordered peptide macrocycles.

scientific article

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

scientific article published on 13 May 2015

Computation of conformational coupling in allosteric proteins

scientific article

Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold

scientific article

Computational Design of Catalytic Dyads and Oxyanion Holes for Ester Hydrolysis

scientific article

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

scientific article

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

scientific article

Computational Design of a Protein-Based Enzyme Inhibitor

scientific article

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

scientific article

Computational Design of an Unnatural Amino Acid Dependent Metalloprotein with Atomic Level Accuracy

scientific article

Computational design of a homotrimeric metalloprotein with a trisbipyridyl core

scientific article published on 08 December 2016

Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface

scientific article

Computational design of a pH-sensitive IgG binding protein

scientific article

Computational design of a red fluorophore ligase for site-specific protein labeling in living cells

scientific article

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

scientific article published on 18 March 2020

Computational design of enone-binding proteins with catalytic activity for the Morita-Baylis-Hillman reaction

scientific article published on 30 January 2013

Computational design of environmental sensors for the potent opioid fentanyl.

scientific article published on 19 September 2017

Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope

scientific article

Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope

scientific article

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

scientific article

Computational design of novel protein binders and experimental affinity maturation

scientific article published on January 2013

Computational design of orthogonal nucleoside kinases

scientific article published on 19 October 2010

Computational design of self-assembling cyclic protein homo-oligomers

scientific article published on 05 December 2016

Computational design of transmembrane pores

scientific article published on 26 August 2020

Computational enzyme design

scientific article published on 25 March 2013

Computational protein design enables a novel one-carbon assimilation pathway.

scientific article

Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis

scientific article

Computational redesign of endonuclease DNA binding and cleavage specificity

scientific article

Computational redesign of protein-protein interaction specificity

scientific article

Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs

scientific article

Computational thermostabilization of an enzyme

scientific article published on May 2005

Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition

scientific article

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

scientific article

Computationally designed libraries for rapid enzyme stabilization

scientific article

Computer-based redesign of a protein folding pathway

scientific article (publication date: July 2001)

Confirmation of intersubunit connectivity and topology of designed protein complexes by native MS.

scientific article published on 19 January 2018

Conserved residue clustering and protein structure prediction.

scientific article

Consistent blind protein structure generation from NMR chemical shift data

scientific article

Contact order and ab initio protein structure prediction

scientific article

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

scientific article published on September 2003

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

scientific article

Contrasting roles for symmetrically disposed beta-turns in the folding of a small protein.

scientific article published in December 1997

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

scientific article

Contributions of solvent–solvent hydrogen bonding and van der Waals interactions to the attraction between methane molecules in water

scientific article published on 01 April 1998

Control of repeat-protein curvature by computational protein design

scientific article

Control over overall shape and size in de novo designed proteins

scientific article

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

scientific article

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

scientific article

Cooperative hydrogen bonding in amyloid formation

scientific article published on 27 February 2007

Critical role of beta-hairpin formation in protein G folding

scientific article published in August 2000

Cryo-EM model validation using independent map reconstructions

scientific article

Cryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure

scientific article

Crystal structure of Toll-like receptor adaptor MAL/TIRAP reveals the molecular basis for signal transduction and disease protection

scientific article

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

scientific article

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

scientific article

Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging

scientific article published on 2 May 2006

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

scientific article

Crystallization and preliminary X-ray diffraction studies of mutants of B1 IgG-binding domain of protein L from Peptostreptococcus magnus

scientific article published on 01 April 2000

De Novo Prediction of Three-dimensional Structures for Major Protein Families

scientific article published on 01 September 2002

De novo computational design of retro-aldol enzymes

scientific article

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

scientific article

De novo design of a homo-trimeric amantadine-binding protein

scientific article published on 19 December 2019

De novo design of a non-local β-sheet protein with high stability and accuracy

scientific article published on 29 October 2018

De novo design of immunoglobulin-like domains

scientific article published in 2022

De novo design of modular and tunable allosteric biosensors

scientific article published on 20 July 2020

De novo design of modular and tunable protein biosensors

scientific article published on 27 January 2021

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

scientific article published on 09 September 2020

De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity

scientific article

De novo design of protein logic gates

scientific article published on 01 April 2020

De novo design of self-assembling helical protein filaments

scientific article published in Science

De novo design of tunable, pH-driven conformational changes.

scientific article published on 01 May 2019

De novo design of tyrosine and serine kinase-driven protein switches

scientific article published on 13 September 2021

De novo designed proteins neutralize lethal snake venom toxins

scientific article published on 15 January 2025

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

scientific article

De novo protein structure generation from incomplete chemical shift assignments.

scientific article

De novo structure generation using chemical shifts for proteins with high-sequence identity but different folds

scientific article

De novo-designed enzymes as small-molecule-regulated fluorescence imaging tags and fluorescent reporters

scientific article published on 11 September 2014

Deciphering a novel thioredoxin-like fold family

scholarly article by Lisa N. Kinch published in June 2003

Design and Characterization of Stabilized Derivatives of Human CD4D12 and CD4D1

article

Design of a Novel Globular Protein Fold with Atomic-Level Accuracy

scientific article

Design of a hyperstable 60-subunit protein dodecahedron. [corrected]

scientific article published on 15 June 2016

Design of activated serine–containing catalytic triads with atomic-level accuracy

scientific article

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

scientific article published in Science

Design of protein-binding proteins from the target structure alone

scientific article published on 24 March 2022

Design of stimulus-responsive two-state hinge proteins

scientific article published on 17 August 2023

Design, activity, and structure of a highly specific artificial endonuclease

scientific article

Designed protein aggregates entrapping carbon nanotubes for bioelectrochemical oxygen reduction

scientific article published on 19 April 2016

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

scientific article published on 20 August 2020

Designed proteins assemble antibodies into modular nanocages

scientific article published on 01 December 2020

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

scientific article published on 19 May 2015

Detection of protein coding sequences using a mixture model for local protein amino acid sequence

scientific article published in February 2000

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

scientific article

Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings

scientific article

Determining crystal structures through crowdsourcing and coursework

scientific article

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

scientific article

Distributions of beta sheets in proteins with application to structure prediction.

scientific article

Efficient minimization of angle-dependent potentials for polypeptides in internal coordinates

article

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

scientific article published on 27 July 2012

Electron density redistribution accounts for half the cooperativity of alpha helix formation

scientific article published in March 2006

Elicitation of structure-specific antibodies by epitope scaffolds

scientific article

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

scientific article published on 29 August 2016

Emergence of symmetry in homooligomeric biological assemblies.

scholarly article

Enantioselective enzymes by computational design and in silico screening

scientific article published on 4 February 2015

Engineering V-type nerve agents detoxifying enzymes using computationally focused libraries

scientific article

Engineering an allosteric transcription factor to respond to new ligands

scientific article published on 21 December 2015

Engineering and design

scientific article published on 01 August 1999

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

scientific article

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

scientific article

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

scientific article published on 19 September 2019

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

scientific article published on 29 November 2021

Evaluation and optimization of discrete state models of protein folding

scientific article

Evaluation and ranking of enzyme designs

scientific article

Evaluation of Models of Electrostatic Interactions in Proteins

article

Evaluation of structural and evolutionary contributions to deleterious mutation prediction

scientific article published in September 2002

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

scientific article

Evolutionary conservation in protein folding kinetics

scientific article published in April 2000

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

scientific article

Expanding the product profile of a microbial alkane biosynthetic pathway

scientific article published on 26 September 2012

Expansive discovery of chemically diverse structured macrocyclic oligoamides

scientific article published on 25 April 2024

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

scientific article

Exploitation of binding energy for catalysis and design

scientific article published on October 2009

Exploration of Alternate Catalytic Mechanisms and Optimization Strategies for Retroaldolase Design

scientific article

Exploring folding free energy landscapes using computational protein design.

scientific article

Exploring the repeat protein universe through computational protein design

scientific article published on 16 December 2015

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

article published in the Proceedings of the National Academy of Sciences of the United States of America

Feature space resampling for protein conformational search.

scientific article

FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants

scientific article published on 3 November 2015

Folding Dynamics of the src SH3 Domain ⬇️

scientific article published on December 16, 1997

Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals

scholarly article

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

scientific article published on 12 February 2021

Free modeling with Rosetta in CASP6

scientific article

Functional inferences from blind ab initio protein structure predictions.

scientific article

Functional rapidly folding proteins from simplified amino acid sequences.

scientific article published on October 1997

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

scientific article

Generalized biomolecular modeling and design with RoseTTAFold All-Atom

scientific article published on 07 March 2024

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

scientific article published on July 2017

HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins.

scientific article

Hallucinating symmetric protein assemblies ⬇️

scientific article published on 15 September 2022

Heterologous epitope-scaffold prime:boosting immuno-focuses B cell responses to the HIV-1 gp41 2F5 neutralization determinant

scientific article

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

scientific article

High thermodynamic stability of parametrically designed helical bundles

scientific article published on October 2014

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

scientific article

High-Throughput Characterization of Protein-Protein Interactions by Reprogramming Yeast Mating

High-accuracy refinement using Rosetta in CASP13

scientific article published on 05 August 2019

High-resolution comparative modeling with RosettaCM.

scientific article published on 12 September 2013

High-resolution mapping of protein sequence-function relationships

scientific article

High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design

scientific article

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

scientific article

High-resolution structure of a retroviral protease folded as a monomer

scientific article published on 19 October 2011

High-resolution structure of the Shigella type-III secretion needle by solid-state NMR and cryo-electron microscopy

scientific article

High-resolution structure prediction and the crystallographic phase problem

scientific article

Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection

scientific article

Hotspot-centric de novo design of protein binders

scientific article

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

scientific article

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

scientific article published on August 1, 1998

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

scientific article

Improved chemical shift based fragment selection for CS-Rosetta using Rosetta3 fragment picker

scientific article

Improved low-resolution crystallographic refinement with Phenix and Rosetta

scientific article

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

scientific article

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

scientific article (publication date: 26 May 2011)

Improved protein structure prediction using predicted interresidue orientations

scientific article published on 02 January 2020

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

scientific article published on 01 January 1999

Improved side-chain modeling for protein-protein docking

scientific article

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

scientific article

Improvement of a potential anthrax therapeutic by computational protein design

scientific article published on 18 July 2011

Improving 3D structure prediction from chemical shift data

scientific article

Improving NMR protein structure quality by Rosetta refinement: A molecular replacement study

scientific article

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

scientific article

Improving the Catalytic Performance of an Artificial Metalloenzyme by Computational Design

scientific article

Incorporation of evolutionary information into Rosetta comparative modeling

scientific article published on 2 June 2011

Increased Diels-Alderase activity through backbone remodeling guided by Foldit players

scientific article

Influenza hemagglutinin: kinetic control of protein function.

scientific article published on October 1994

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

scientific article

Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway

scientific article

Interactions of the transmembrane polymeric rings of the Salmonella enterica serovar Typhimurium type III secretion system

scientific article

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

scientific article published on 01 June 2019

Intrinsic disorder drives N-terminal ubiquitination by Ube2w

scientific article

Introduction of a polar core into the de novo designed protein Top7.

scientific article published on 13 February 2016

Kemp elimination catalysts by computational enzyme design

scientific article

Kinetics of Folding of the IgG Binding Domain of Peptostreptoccocal Protein L

article

Large-scale determination of previously unsolved protein structures using evolutionary information

scientific article

Local interactions and the optimization of protein folding ⬇️

scientific article published on November 1, 1997

Long-range order in the src SH3 folding transition state

scientific article published on June 2000

Low free energy cost of very long loop insertions in proteins

scientific article

Macromolecular modeling and design in Rosetta: recent methods and frameworks

scientific article published on 01 June 2020

Massively parallel determination and modeling of endonuclease substrate specificity

scientific article

Mechanistic Analysis of an Engineered Enzyme that Catalyzes the Formose Reaction.

scientific article

Metastable states and folding free energy barriers

Mining endonuclease cleavage determinants in genomic sequence data.

scientific article

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

scientific article published on 4 August 2006

Modeling symmetric macromolecular structures in Rosetta3

scientific article

Modular repeat protein sculpting using rigid helical junctions

scientific article published on 03 April 2020

Modulation of integrin activation by an entropic spring in the {beta}-knee

scientific article

Motif-directed flexible backbone design of functional interactions

scientific article

Multipass membrane protein structure prediction using Rosetta

scientific article

Multiplex pairwise assembly of array-derived DNA oligonucleotides

scientific article published on 8 November 2015

Multivalent Display of Antifreeze Proteins by Fusion to Self-Assembling Protein Cages Enhances Ice-Binding Activities

scientific article published on 29 November 2016

Mutations designed to destabilize the receptor-bound conformation increase MICA-NKG2D association rate and affinity

scientific article

NMR characterization of residual structure in the denatured state of protein L

NMR structure determination for larger proteins using backbone-only data

scientific article

Native protein sequences are close to optimal for their structures

scientific article

Networks of electrostatic and hydrophobic interactions modulate the complex folding free energy surface of a designed βα protein

scientific article published on 15 March 2019

New algorithms and an in silico benchmark for computational enzyme design

scientific article published on December 2006

Nonnative Interactions in the FF Domain Folding Pathway from an Atomic Resolution Structure of a Sparsely Populated Intermediate: An NMR Relaxation Dispersion Study

scientific article

On the role of a conserved, potentially helix-breaking residue in the tRNA-binding alpha-helix of archaeal CCA-adding enzymes

scientific article published on 21 May 2008

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

scientific article

Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing

scientific article

Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution

scientific article

P05-09. 4e10 epitope-scaffolds mimic the antibody-bound epitope conformation and block neutralization by sera from rare HIV+ individuals

scientific article published on 22 October 2009

PRISM: topologically constrained phased refinement for macromolecular crystallography

scientific article published in September 1993

Physically realistic homology models built with ROSETTA can be more accurate than their templates

scholarly article

Post-translational modification of the N-terminal His tag interferes with the crystallization of the wild-type and mutant SH3 domains from chicken src tyrosine kinase.

scientific article

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

scientific article published on 9 December 2015

Predicting protein structures with a multiplayer online game

scientific article

Prediction and design of macromolecular structures and interactions

scientific article

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

scientific article

Prediction of CASP6 structures using automated Robetta protocols

scientific article

Prediction of local structure in proteins using a library of sequence-structure motifs ⬇️

scientific article published on August 21, 1998

Prediction of membrane protein structures with complex topologies using limited constraints

scientific article

Prediction of structures of multidomain proteins from structures of the individual domains

scientific article published on 22 December 2006

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

scientific article

Prediction of the structure of symmetrical protein assemblies

scholarly article

Principles for designing ideal protein structures

scientific article

Principles for designing proteins with cavities formed by curved β sheets

scientific article published on January 2017

Profile-profile comparisons by COMPASS predict intricate homologies between protein families

scientific article

Progress and challenges in high-resolution refinement of protein structure models.

scientific article

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

scientific article

Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus

scientific article

Proof of principle for epitope-focused vaccine design

scientific article

Prospects for de novo phasing with de novo protein models

scientific article published on 20 January 2009

Protease pro region required for folding is a potent inhibitor of the mature enzyme.

scientific article published in April 1992

Protein NMR structures refined with Rosetta have higher accuracy relative to corresponding X-ray crystal structures

scientific article

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

scientific article published on 17 May 2016

Protein homology model refinement by large-scale energy optimization.

scientific article published on 5 March 2018

Protein interaction networks revealed by proteome coevolution

scientific article published on 11 July 2019

Protein structure determination from pseudocontact shifts using ROSETTA.

scientific article

Protein structure determination using metagenome sequence data

scientific article

Protein structure prediction and analysis using the Robetta server.

scientific article

Protein structure prediction in 2002.

scientific article

Protein transport to the vacuole and receptor-mediated endocytosis by clathrin heavy chain-deficient yeast

scientific article

Protein-DNA binding specificity predictions with structural models

scientific article

Protein-protein docking predictions for the CAPRI experiment

scientific article (publication date: July 2003)

Protein-protein docking with backbone flexibility

scientific article published on 2 August 2007

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

scientific article (publication date: August 2003)

Quantitative reactivity profiling predicts functional cysteines in proteomes

scientific article

ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility

scientific article published in November 2006

Ranking predicted protein structures with support vector regression.

scientific article

Rational HIV Immunogen Design to Target Specific Germline B Cell Receptors

scientific article

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

scientific article

Rationally designed integrin beta3 mutants stabilized in the high affinity conformation

scientific article published on 19 November 2008

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

scientific article published on 7 May 2004

Recapitulation and design of protein binding peptide structures and sequences

scientific article published on 31 January 2006

Recapitulation of protein family divergence using flexible backbone protein design

scientific article

Receptor subtype discrimination using extensive shape complementary designed interfaces

scientific article published on 13 May 2019

Recombinant immunotoxin for cancer treatment with low immunogenicity by identification and silencing of human T-cell epitopes

scientific article

Reconstitution of SEC gene product-dependent intercompartmental protein transport

scientific article

Reconstitution of intercompartmental protein transport in yeast extracts

PhD thesis by David Baker

Recurring local sequence motifs in proteins.

scientific article

Redesigning the specificity of protein-DNA interactions with Rosetta

scientific article

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

scientific article published on 08 July 2009

Relaxation of backbone bond geometry improves protein energy landscape modeling

scientific article published on January 2014

Remodeling a β-peptide bundle

article

Removing T-cell epitopes with computational protein design.

scientific article

Reprogramming homing endonuclease specificity through computational design and directed evolution

scientific article

Rescue of Degradation-Prone Mutants of the FK506-Rapamycin Binding (FRB) Protein with Chemical Ligands

scholarly article by Kryn Stankunas published in July 2007

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

scientific article published in February 2002

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

scientific article

Restricted sidechain plasticity in the structures of native proteins and complexes

scientific article

Robust deep learning–based protein sequence design using ProteinMPNN ⬇️

scientific article published on 15 September 2022

Robust design and optimization of retroaldol enzymes.

scientific article published on 30 March 2012

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

scientific article

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

scientific article published on April 13, 2012

Rosetta in CAPRI rounds 13-19. ⬇️

scientific article published on November 2010

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

scientific article

RosettaDock in CAPRI rounds 6-12

scientific article (publication date: December 2007)

RosettaHoles2: a volumetric packing measure for protein structure refinement and validation

scientific article

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

scientific article published on January 2009

RosettaLigand docking with full ligand and receptor flexibility

scientific article published on 18 November 2008

RosettaRemodel: a generalized framework for flexible backbone protein design.

scientific article

RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite

scientific article (publication date: 2011)

Sampling bottlenecks in de novo protein structure prediction

scientific article

Scaffolding protein functional sites using deep learning ⬇️

scientific article published on 22 July 2022

Scientific benchmarks for guiding macromolecular energy function improvement

scientific article (publication date: 2013)

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

scientific article

Self-assembly-based posttranslational protein oscillators

scientific article published on 16 December 2020

Simple physical models connect theory and experiment in protein folding kinetics

scientific article published in September 2002

Simple yet functional phosphate-loop proteins

scientific article published on 30 November 2018

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

scientific article

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

scientific article

Simultaneous prediction of protein folding and docking at high resolution

scientific article published on 28 October 2009

Single-site mutations induce 3D domain swapping in the B1 domain of protein L from Peptostreptococcus magnus

scientific article

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

scientific article

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

scientific article

Strand-loop-strand motifs: prediction of hairpins and diverging turns in proteins

scientific article published in February 2004

Structural Analyses of Covalent Enzyme–Substrate Analog Complexes Reveal Strengths and Limitations of De Novo Enzyme Design

scientific article

Structural Transitions in the Protein L Denatured State Ensemble

scientific article published on 01 November 1999

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

scientific article

Structural and functional evaluation of de novo-designed, two-component nanoparticle carriers for HIV Env trimer immunogens

scientific article published on 11 August 2020

Structural and kinetic characterization of the simplified SH3 domain FP1.

scientific article

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

scientific article published on 12 December 2011

Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus

scientific article

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

scholarly article

Structural plasticity of helical nanotubes based on coiled-coil assemblies

scientific article

Structure of Lmaj006129AAA, a hypothetical protein from Leishmania major

scientific article

Structure of a designed tetrahedral protein assembly variant engineered to have improved soluble expression

scientific article

Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 Å resolution

scientific article

Structure of the BamC Two-Domain Protein Obtained by Rosetta with a Limited NMR Data Set

scientific article

Structure of the type VI secretion system contractile sheath

scientific article

Structure of the ultra-high-affinity colicin E2 DNase--Im2 complex

scientific article

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

scientific article

Structure prediction for CASP8 with all-atom refinement using Rosetta.

scientific article

Structure similarity measure with penalty for close non-equivalent residues

scientific article published on 25 March 2009

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

scientific article

Structure-guided forcefield optimization

scientific article published on 12 April 2011

Structures of the B1 domain of protein L from Peptostreptococcus magnus with a tyrosine to tryptophan substitution

scientific article

Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology

scientific article

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

scientific article published on 04 August 2020

The Acidic Transcription Activator Gcn4 Binds the Mediator Subunit Gal11/Med15 Using a Simple Protein Interface Forming a Fuzzy Complex

scientific article

The Effects of Mutations on Motions of Side-chains in Protein L Studied by 2H NMR Dynamics and Scalar Couplings

article

The Highly Cooperative Folding of Small Naturally Occurring Proteins Is Likely the Result of Natural Selection

article by Alexander L. Watters et al published February 2007 in Cell

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

scientific article

The coming of age of de novo protein design

scientific article published on 14 September 2016

The common structural architecture of Shigella flexneri and Salmonella typhimurium type three secretion needles

scientific article

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

scientific article

The dynamic disulphide relay of quiescin sulphydryl oxidase

scientific article

The effect of ultrasound-induced hyperthermia and X irradiation on skin

scientific article published on 01 November 1983

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

scientific article

The origin of consistent protein structure refinement from structural averaging.

scientific article

The role of pro regions in protein folding.

scientific article

The sequences of small proteins are not extensively optimized for rapid folding by natural selection

scientific article

The single helix in protein L is largely disrupted at the rate-limiting step in folding

scientific article published in December 1998

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

scientific article

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

scientific article published on April 2009

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

scientific article published on December 2007

Thermodynamically coupled biosensors for detecting neutralizing antibodies against SARS-CoV-2 variants

scientific article published in 2022

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

scientific article published on 17 November 2020

Top-down design of protein architectures with reinforcement learning

scientific article published on 20 April 2023

Topological control of cytokine receptor signaling induces differential effects in hematopoiesis

scientific article

Toward high-resolution prediction and design of transmembrane helical protein structures

scholarly article

Transition states. Trapping a transition state in a computationally designed protein bottle

scientific article

Two common structural motifs for TCR recognition by staphylococcal enterotoxins

scientific article

Two-Component Sensor RhpS Promotes Induction of Pseudomonas syringae Type III Secretion System by Repressing Negative Regulator RhpR

scientific article published on 01 March 2007

Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects

scientific article

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

scientific article published on 13 July 2015

Uniqueness and the ab initio phase problem in macromolecular crystallography.

scientific article published in January 1993

WeFold: a coopetition for protein structure prediction

scientific article

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

scientific article

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