List of works - Tanja Kortemme

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

scientific article published in March 2005

A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family

scientific article

A Mechanism for Tunable Autoinhibition in the Structure of a Human Ca2+/Calmodulin- Dependent Kinase II Holoenzyme

scientific article

A Model for the Molecular Mechanism of an Engineered Light-Driven Protein Machine

scientific article

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

scientific article

A Ras-induced conformational switch in the Ras activator Son of sevenless

scientific article (publication date: 7 November 2006)

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

scientific article published on 30 April 2020

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing ⬇️

journal article from 'bioRxiv' published in 2020

A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design

scientific article (publication date: 2015)

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

scientific article (publication date: 2004)

A simple model of backbone flexibility improves modeling of side-chain conformational variability

scientific article (publication date: 18 July 2008)

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

scientific article (publication date: 29 October 2002)

Accurate positioning of functional residues with robotics-inspired computational protein design

scholarly article

Accurately positioning functional residues with robotics-inspired computational protein design

preprint

Altered expression of a quality control protease in E. coli reshapes the in vivo mutational landscape of a model enzyme

scientific article published on 23 July 2020

Amino-acid site variability among natural and designed proteins

scientific article (publication date: 2013)

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

scientific article

Aromatic side-chain contribution to far-ultraviolet circular dichroism of helical peptides and its effect on measurement of helix propensities

scientific article published in June 1993

Assessment of flexible backbone protein design methods for sequence library prediction in the therapeutic antibody Herceptin-HER2 interface

article

Backbone flexibility in computational protein design

scientific article

Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction

scientific article (publication date: 18 July 2008)

Beta-hairpin and beta-sheet formation in designed linear peptides.

scientific article

Better together: Elements of successful scientific software development in a distributed collaborative community

scientific article published on 04 May 2020

Ca2+ indicators based on computationally redesigned calmodulin-peptide pairs

scientific article published in May 2006

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

scientific article (publication date: 4 May 2004)

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

scientific article (publication date: 10 February 2015)

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms

scientific article published on 15 October 2020

Comparison of Rosetta flexible-backbone computational protein design methods on binding interactions

scientific article published on 10 August 2019

Comparison of the (30-51, 14-38) two-disulphide folding intermediates of the homologous proteins dendrotoxin K and bovine pancreatic trypsin inhibitor by two-dimensional 1H nuclear magnetic resonance.

scientific article

Complex topology rather than complex membership is a determinant of protein dosage sensitivity

scientific article (publication date: 2009)

Computational alanine scanning of protein-protein interfaces

scientific article published on 3 February 2004

Computational design of a modular protein sense-response system

scientific article published on 01 November 2019

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 protein-protein interactions

scientific article published on February 2004

Computational design of structured loops for new protein functions

scientific article published in 2019

Computational protein design quantifies structural constraints on amino acid covariation

scientific article (publication date: 2013)

Computational redesign of protein-protein interaction specificity

scientific article

Computer-aided design of functional protein interactions

scientific article

Construction of a genetic multiplexer to toggle between chemosensory pathways in Escherichia coli

scientific article (publication date: 18 February 2011)

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

Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair

scientific article

Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs

scientific article published on 09 May 2019

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

scientific article

Correction to “The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design”

scientific article published on 06 June 2022

Cost-benefit tradeoffs in engineered lac operons

scientific article published in May 2012

Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity

scientific article (publication date: 2015)

De novo protein fold families expand the designable ligand binding site space

scientific article published on 22 November 2021

Deconstruction of the Ras switching cycle through saturation mutagenesis

scientific article

Design of Light-Controlled Protein Conformations and Functions

scientific article (publication date: 2016)

Design of Multi-Specificity in Protein Interfaces

scientific article published on 06 July 2007

Design of a 20-amino acid, three-stranded beta-sheet protein

scientific article published in July 1998

Design of a phosphorylatable PDZ domain with peptide-specific affinity changes

scientific article published on 15 November 2012

Design of a photoswitchable cadherin

scientific article (publication date: 28 August 2013)

Design of multi-specificity in protein interfaces

scientific article (publication date: August 2007)

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

scientific article

Designing ensembles in conformational and sequence space to characterize and engineer proteins

scientific article published on 19 March 2010

Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting

scientific article (publication date: 25 April 2016)

Differences in flexibility underlie functional differences in the Ras activators son of sevenless and Ras guanine nucleotide releasing factor 1

scientific article (publication date: 14 January 2009)

Editorial overview: Engineering and design: raising the bar through innovation and integration

scientific article published on 28 August 2014

Electrostatic interactions in the active site of the N-terminal thioredoxin-like domain of protein disulfide isomerase

scientific article

Engineered ACE2 receptor traps potently neutralize SARS-CoV-2

scientific article published on 01 August 2020

Engineered ACE2 receptor traps potently neutralize SARS-CoV-2

scientific article published on 22 October 2020

Engineered protein connectivity to actin mimics PDZ-dependent recycling of G protein-coupled receptors but not its regulation by Hrs

scientific article (publication date: 23 January 2009)

Engineering a light-activated caspase-3 for precise ablation of neurons in vivo.

scientific article published on 11 September 2017

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

scientific article published on 29 November 2021

Evaluation of Models of Electrostatic Interactions in Proteins

article

Expanding the space of protein geometries by computational design of de novo fold families

scientific article published on 01 August 2020

Expanding the space of protein geometries by computational design of de novo fold families

scientific article published on 15 April 2020

Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance

scientific article published on 23 July 2018

Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein-Protein Binding Affinity upon Mutation

scientific article published on 15 February 2018

Flexible backbone sampling methods to model and design protein alternative conformations

scientific article (publication date: 2013)

Global landscape of HIV-human protein complexes

scientific article

Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions.

scientific article published on May 1994

Improvements to Robotics-Inspired Conformational Sampling in Rosetta ⬇️

scientific article (publication date: 2013)

In support of the BMRB.

scientific article published in September 2012

Ionisation of cysteine residues at the termini of model alpha-helical peptides. Relevance to unusual thiol pKa values in proteins of the thioredoxin family.

scientific article

Ionization-reactivity relationships for cysteine thiols in polypeptides.

scientific article

Macromolecular modeling and design in Rosetta: recent methods and frameworks

scientific article published on 01 June 2020

Multi-constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility

scientific article (publication date: June 2009)

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

scientific article

New computational protein design methods for de novo small molecule binding sites

scientific article published on 05 October 2020

Outcome of a workshop on applications of protein models in biomedical research

scientific article (publication date: 13 February 2009)

Potential functions for hydrogen bonds in protein structure prediction and design.

scientific article

Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design

scientific article (publication date: 2011)

Prediction of mutational tolerance in HIV-1 protease and reverse transcriptase using flexible backbone protein design

scientific article (publication date: 2012)

Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design

scientific article

Protein-protein docking predictions for the CAPRI experiment

scientific article (publication date: July 2003)

Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition

scientific article (publication date: 28 October 2014)

Quantitative mapping of protein-peptide affinity landscapes using spectrally encoded beads

scientific article published on 08 July 2019

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

scientific article (publication date: 2011)

Rational design of intercellular adhesion molecule-1 (ICAM-1) variants for antagonizing integrin lymphocyte function-associated antigen-1-dependent adhesion

scientific article (publication date: 24 February 2006)

Reprogramming an ATP-driven protein machine into a light-gated nanocage

scientific article (publication date: December 2013)

RosettaBackrub--a web server for flexible backbone protein structure modeling and design

scientific article (publication date: July 2010)

SNX27 mediates PDZ-directed sorting from endosomes to the plasma membrane

scientific article

Scientific benchmarks for guiding macromolecular energy function improvement

scientific article (publication date: 2013)

Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE)

scientific article (publication date: 2013)

Similarities between the spectrin SH3 domain denatured state and its folding transition state

scientific article

Simple physical models connect theory and experiment in protein folding kinetics

scientific article published in September 2002

Structural basis for unique mechanisms of folding and hemoglobin binding by a malarial protease

scientific article (publication date: August 2006)

Structural mapping of protein interactions reveals differences in evolutionary pressures correlated to mRNA level and protein abundance

scientific article (publication date: November 2007)

Structure-based prediction of the peptide sequence space recognized by natural and synthetic PDZ domains

scientific article published on 21 July 2010

Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling

scientific article (publication date: August 2009)

Symmetry Recognizing Asymmetry

scientific article (publication date: April 2003)

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

scientific article (publication date: April 2003)

Systems-level effects of allosteric perturbations to a model molecular switch

scientific article published on 13 October 2021

The Global Phosphorylation Landscape of SARS-CoV-2 Infection

scientific article published on 28 June 2020

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design.

scientific article published on 21 April 2017

The design of linear peptides that fold as monomeric beta-sheet structures.

scientific article

List of works by Tanja Kortemme

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

A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family

A Mechanism for Tunable Autoinhibition in the Structure of a Human Ca2+/Calmodulin- Dependent Kinase II Holoenzyme

A Model for the Molecular Mechanism of an Engineered Light-Driven Protein Machine

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

A Ras-induced conformational switch in the Ras activator Son of sevenless

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing ⬇️

A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design

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

A simple model of backbone flexibility improves modeling of side-chain conformational variability

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

Accurate positioning of functional residues with robotics-inspired computational protein design

Accurately positioning functional residues with robotics-inspired computational protein design

Altered expression of a quality control protease in E. coli reshapes the in vivo mutational landscape of a model enzyme

Amino-acid site variability among natural and designed proteins

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

Aromatic side-chain contribution to far-ultraviolet circular dichroism of helical peptides and its effect on measurement of helix propensities

Assessment of flexible backbone protein design methods for sequence library prediction in the therapeutic antibody Herceptin-HER2 interface

Backbone flexibility in computational protein design

Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction

Beta-hairpin and beta-sheet formation in designed linear peptides.

Better together: Elements of successful scientific software development in a distributed collaborative community

Ca2+ indicators based on computationally redesigned calmodulin-peptide pairs

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

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

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms

Comparison of Rosetta flexible-backbone computational protein design methods on binding interactions

Comparison of the (30-51, 14-38) two-disulphide folding intermediates of the homologous proteins dendrotoxin K and bovine pancreatic trypsin inhibitor by two-dimensional 1H nuclear magnetic resonance.

Complex topology rather than complex membership is a determinant of protein dosage sensitivity

Computational alanine scanning of protein-protein interfaces

Computational design of a modular protein sense-response system

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

Computational design of protein-protein interactions

Computational design of structured loops for new protein functions

Computational protein design quantifies structural constraints on amino acid covariation

Computational redesign of protein-protein interaction specificity

Computer-aided design of functional protein interactions

Construction of a genetic multiplexer to toggle between chemosensory pathways in Escherichia coli

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

Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair

Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs

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

Correction to “The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design”

Cost-benefit tradeoffs in engineered lac operons

Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity

De novo protein fold families expand the designable ligand binding site space

Deconstruction of the Ras switching cycle through saturation mutagenesis

Design of Light-Controlled Protein Conformations and Functions

Design of Multi-Specificity in Protein Interfaces

Design of a 20-amino acid, three-stranded beta-sheet protein

Design of a phosphorylatable PDZ domain with peptide-specific affinity changes

Design of a photoswitchable cadherin

Design of multi-specificity in protein interfaces

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

Designing ensembles in conformational and sequence space to characterize and engineer proteins

Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting

Differences in flexibility underlie functional differences in the Ras activators son of sevenless and Ras guanine nucleotide releasing factor 1

Editorial overview: Engineering and design: raising the bar through innovation and integration

Electrostatic interactions in the active site of the N-terminal thioredoxin-like domain of protein disulfide isomerase

Engineered ACE2 receptor traps potently neutralize SARS-CoV-2

Engineered ACE2 receptor traps potently neutralize SARS-CoV-2

Engineered protein connectivity to actin mimics PDZ-dependent recycling of G protein-coupled receptors but not its regulation by Hrs

Engineering a light-activated caspase-3 for precise ablation of neurons in vivo.

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

Evaluation of Models of Electrostatic Interactions in Proteins

Expanding the space of protein geometries by computational design of de novo fold families

Expanding the space of protein geometries by computational design of de novo fold families

Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance

Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein-Protein Binding Affinity upon Mutation

Flexible backbone sampling methods to model and design protein alternative conformations

Global landscape of HIV-human protein complexes

Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions.

Improvements to Robotics-Inspired Conformational Sampling in Rosetta ⬇️

In support of the BMRB.

Ionisation of cysteine residues at the termini of model alpha-helical peptides. Relevance to unusual thiol pKa values in proteins of the thioredoxin family.

Ionization-reactivity relationships for cysteine thiols in polypeptides.

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Multi-constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility