Tanja Kortemme
#95,772
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Computational biologist
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Tanja Kortemmebiology Degrees
Biology
#8717
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#11842
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Computational Biology
#326
World Rank
#327
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Biology
Tanja Kortemme's Degrees
- PhD Biophysics University of California, San Francisco
Why Is Tanja Kortemme Influential?
(Suggest an Edit or Addition)According to Wikipedia, Tanja Kortemme is a bioengineering professor at University of California, San Francisco. She has been recognized for outstanding contributions in computational protein design, including energy functions, sampling algorithms, and molecules to rewire cellular control circuits. She was an inaugural Chan Zuckerberg Biohub investigator and was inducted into American Institute for Medical and Biological Engineering College of Fellows.
Tanja Kortemme's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug-Repurposing (2020) (3012)
- ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. (2011) (1504)
- A simple physical model for binding energy hot spots in protein–protein complexes (2002) (789)
- The Rosetta all-atom energy function for macromolecular modeling and design (2017) (788)
- The Global Phosphorylation Landscape of SARS-CoV-2 Infection (2020) (651)
- Global landscape of HIV–human protein complexes (2011) (645)
- Helix propensities of the amino acids measured in alanine‐based peptides without helix‐stabilizing side‐chain interactions (1994) (537)
- Computational Alanine Scanning of Protein-Protein Interfaces (2004) (496)
- Ca2+ indicators based on computationally redesigned calmodulin-peptide pairs. (2006) (492)
- An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. (2003) (485)
- A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing (2020) (456)
- Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms (2020) (444)
- Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling (2009) (418)
- Ionization-reactivity relationships for cysteine thiols in polypeptides. (1998) (362)
- Macromolecular modeling and design in Rosetta: recent methods and frameworks (2020) (339)
- Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE) (2013) (302)
- Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. (2008) (296)
- Computational redesign of protein-protein interaction specificity (2004) (292)
- Ionisation of cysteine residues at the termini of model alpha-helical peptides. Relevance to unusual thiol pKa values in proteins of the thioredoxin family. (1995) (288)
- Design of a 20-Amino Acid, Three-Stranded β-Sheet Protein (1998) (270)
- Aromatic side-chain contribution to far-ultraviolet circular dichroism of helical peptides and its effect on measurement of helix propensities. (1993) (270)
- Design, activity, and structure of a highly specific artificial endonuclease. (2002) (248)
- Computational design of protein-protein interactions. (2004) (245)
- SNX27 mediates PDZ-directed sorting from endosomes to the plasma membrane (2010) (226)
- Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. (2004) (221)
- Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta. (2015) (202)
- A Mechanism for Tunable Autoinhibition in the Structure of a Human Ca2+/Calmodulin- Dependent Kinase II Holoenzyme (2011) (202)
- Scientific benchmarks for guiding macromolecular energy function improvement. (2013) (191)
- Computer-aided design of functional protein interactions. (2009) (176)
- Improvements to Robotics-Inspired Conformational Sampling in Rosetta (2013) (152)
- Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface. (2006) (151)
- A “solvated rotamer” approach to modeling water‐mediated hydrogen bonds at protein–protein interfaces (2005) (146)
- Convergent mechanisms for recognition of divergent cytokines by the shared signaling receptor gp130. (2003) (133)
- A Ras-induced conformational switch in the Ras activator Son of sevenless (2006) (130)
- Outcome of a workshop on applications of protein models in biomedical research. (2009) (129)
- Electrostatic interactions in the active site of the N-terminal thioredoxin-like domain of protein disulfide isomerase. (1996) (122)
- Symmetry recognizing asymmetry: analysis of the interactions between the C-type lectin-like immunoreceptor NKG2D and MHC class I-like ligands. (2003) (120)
- Protein–protein docking predictions for the CAPRI experiment (2003) (113)
- RosettaBackrub—a web server for flexible backbone protein structure modeling and design (2010) (109)
- Structure-based prediction of the peptide sequence space recognized by natural and synthetic PDZ domains. (2010) (109)
- Design of Multi-Specificity in Protein Interfaces (2007) (107)
- Backbone flexibility in computational protein design. (2009) (107)
- The design of linear peptides that fold as monomeric β-sheet structures (1999) (103)
- Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs (2018) (103)
- Engineered ACE2 receptor traps potently neutralize SARS-CoV-2 (2020) (102)
- Predicting the Tolerated Sequences for Proteins and Protein Interfaces Using RosettaBackrub Flexible Backbone Design (2011) (100)
- Cost-Benefit Tradeoffs in Engineered lac Operons (2012) (98)
- β-hairpin and β-sheet formation in designed linear peptides (1999) (93)
- Structural basis for unique mechanisms of folding and hemoglobin binding by a malarial protease. (2006) (89)
- Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein-Protein Binding Affinity upon Mutation. (2018) (89)
- Engineered ACE2 receptor traps potently neutralize SARS-CoV-2 (2020) (87)
- Flex ddG: Rosetta ensemble-based estimation of changes in protein-protein binding affinity upon mutation (2017) (82)
- Similarities between the spectrin SH3 domain denatured state and its folding transition state. (2000) (82)
- Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design. (2008) (81)
- Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair (2012) (81)
- Simple physical models connect theory and experiment in protein folding kinetics. (2002) (79)
- A simple model of backbone flexibility improves modeling of side-chain conformational variability. (2008) (79)
- Deconstruction of the Ras switching cycle through saturation mutagenesis (2017) (78)
- A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family (2009) (77)
- A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design (2015) (73)
- A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys. (2004) (71)
- Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity (2015) (65)
- Design of a 20-amino acid, three-stranded beta-sheet protein. (1998) (63)
- Construction of a genetic multiplexer to toggle between chemosensory pathways in Escherichia coli. (2011) (63)
- Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting (2015) (63)
- Bi-paratopic and multivalent VH domains block ACE2 binding and neutralize SARS-CoV-2 (2020) (62)
- Rational Design of Intercellular Adhesion Molecule-1 (ICAM-1) Variants for Antagonizing Integrin Lymphocyte Function-associated Antigen-1-dependent Adhesion* (2006) (59)
- Potential functions for hydrogen bonds in protein structure prediction and design. (2005) (56)
- Recent advances in de novo protein design: Principles, methods, and applications (2021) (56)
- Multi‐constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility (2009) (50)
- Evaluation of Models of Electrostatic Interactions in Proteins (2003) (50)
- Computational design of a modular protein sense-response system (2019) (48)
- Reprogramming an ATP-driven protein machine into a light-gated nanocage (2013) (46)
- CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. (2021) (45)
- Flexible backbone sampling methods to model and design protein alternative conformations. (2013) (44)
- A SARS-CoV-2 protein interaction map reveals targets for drug repurposing (2020) (43)
- Engineering a light-activated caspase-3 for precise ablation of neurons in vivo (2017) (39)
- Computational Protein Design Quantifies Structural Constraints on Amino Acid Covariation (2013) (36)
- A Mechanism for Tunable Autoinhibition in the Structure of a Human Ca2+/Calmodulin- Dependent Kinase II Holoenzyme (2011) (35)
- Assessment of flexible backbone protein design methods for sequence library prediction in the therapeutic antibody Herceptin–HER2 interface (2011) (35)
- Expanding the space of protein geometries by computational design of de novo fold families (2020) (34)
- Quantitative mapping of protein-peptide affinity landscapes using spectrally encoded beads (2018) (34)
- Structural mapping of protein interactions reveals differences in evolutionary pressures correlated to mRNA level and protein abundance. (2007) (29)
- Mutations Designed to Destabilize the Receptor-Bound Conformation Increase MICA-NKG2D Association Rate and Affinity* (2007) (27)
- Designing ensembles in conformational and sequence space to characterize and engineer proteins. (2010) (27)
- Beta-hairpin and beta-sheet formation in designed linear peptides. (1999) (25)
- Contributions of amino acid side chains to the kinetics and thermodynamics of the bivalent binding of protein L to Ig kappa light chain. (2004) (22)
- Differences in flexibility underlie functional differences in the Ras activators son of sevenless and Ras guanine nucleotide releasing factor 1. (2009) (22)
- Computational design of a modular protein sense/response system (2019) (22)
- Complex topology rather than complex membership is a determinant of protein dosage sensitivity (2009) (21)
- Prediction of Mutational Tolerance in HIV-1 Protease and Reverse Transcriptase Using Flexible Backbone Protein Design (2012) (21)
- Computational design of structured loops for new protein functions (2019) (20)
- A New Twist in TCR Diversity Revealed by a Forbidden αβ TCR (2008) (20)
- Comparison of Rosetta flexible‐backbone computational protein design methods on binding interactions (2020) (20)
- Altered expression of a quality control protease in E. coli reshapes the in vivo mutational landscape of a model enzyme (2020) (19)
- Design of a phosphorylatable PDZ domain with peptide-specific affinity changes. (2013) (19)
- Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition (2014) (18)
- The design of linear peptides that fold as monomeric beta-sheet structures. (1999) (18)
- Engineered Protein Connectivity to Actin Mimics PDZ-dependent Recycling of G Protein-coupled Receptors but Not Its Regulation by Hrs* (2009) (18)
- Better together: Elements of successful scientific software development in a distributed collaborative community (2020) (17)
- Design of a Photoswitchable Cadherin (2013) (17)
- Amino-acid site variability among natural and designed proteins (2013) (16)
- Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance (2018) (14)
- A new twist in TCR diversity revealed by a forbidden alphabeta TCR. (2008) (14)
- Design principles of protein switches. (2021) (13)
- New computational protein design methods for de novo small molecule binding sites (2020) (12)
- SAT-based protein design (2009) (10)
- Systems-level effects of allosteric perturbations to a model molecular switch (2021) (7)
- CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. (2021) (7)
- 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. (1996) (7)
- In support of the BMRB (2012) (7)
- A Model for the Molecular Mechanism of an Engineered Light-Driven Protein Machine. (2016) (6)
- Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks (2021) (5)
- Comparison of Rosetta flexible-backbone computational protein design methods on binding interactions (2019) (5)
- Macromolecular modeling and design in Rosetta: recent methods and frameworks (2020) (5)
- A Mechanism for Tunable Autoinhibition in the Structure of a Human Ca 2+/Calmodulin- Dependent Kinas (2011) (4)
- Design of Light-Controlled Protein Conformations and Functions. (2016) (3)
- Symmetry Recognizing Asymmetry : Analysis of the Interactions between the C-Type Lectin-like Immunoreceptor NKG 2 D and MHC Class (2003) (3)
- Accurate positioning of functional residues with robotics-inspired computational protein design (2022) (3)
- Discovering novel calcineurin inhibitors through quantitative mapping of protein-peptide affinity landscapes (2018) (3)
- Reply to Liu et al.: Specific mutations matter in specificity and catalysis in ACE2 (2021) (2)
- Paper AlertStructural biology (2001) (2)
- A complete allosteric map of a GTPase switch in its native network (2022) (2)
- A complete allosteric map of a GTPase switch in its native cellular network. (2023) (2)
- Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs (2019) (2)
- Advances in the Computational Design of Small-Molecule-Controlled Protein-Based Circuits for Synthetic Biology (2022) (1)
- De novo protein fold families expand the designable ligand binding site space (2021) (1)
- Research Advance: Extending chemical perturbations of the Ubiquitin fitness landscape in a classroom setting (2017) (1)
- Correction to "The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design". (2022) (1)
- Ligand-induced changes in dynamics mediate long-range allostery in the lac repressor (2021) (1)
- Modulating the cellular context broadly reshapes the mutational landscape of a model enzyme (2019) (1)
- Author response: Deconstruction of the Ras switching cycle through saturation mutagenesis (2017) (1)
- Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor (2023) (0)
- Quantitative mapping of 1 protein-peptide affinity landscapes 2 using spectrally encoded beads 3 (2019) (0)
- Structure of designed orthogonal interaction between CDC42 and nucleotide exchange domains of intersectin (2012) (0)
- Genome-wide structural mapping of protein interactions reveals differences in abundance-and expression-dependent evolutionary pressures (2008) (0)
- Computational design of reprogrammed and new protein functions (2017) (0)
- β‐Hairpin and β‐Sheet Formation in Designed Linear Peptides (1999) (0)
- Values Statement: Equality and Inclusion in the RosettaCommons. (2020) (0)
- Specific tests for Rosetta running on our automated testing framework. (2020) (0)
- Semi-explicit Solvation Improves Ligand Binding Site Design in an Allosteric Protein (2020) (0)
- Crystal Structure of the E7_G/Im7_G complex; a designed interface between the colicin E7 DNAse and the Im7 immunity protein (2006) (0)
- Computationally-designed, modular sense/response system (S3-2D) (2019) (0)
- Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps (2022) (0)
- Crystal structure of the E7_C/Im7_C complex; a computationally designed interface between the colicin E7 DNase and the Im7 Immunity protein (2004) (0)
- Reprogramming an ATP-Driven Biological Machine into a Light-Gated Protein Nanocage (2014) (0)
- Computer-aided design of functional protein (2009) (0)
- A Deep-Dive into the Rosetta Energy Function for Biological Macromolecules (2017) (0)
- Editorial overview: Engineering and design: raising the bar through innovation and integration. (2014) (0)
- Members of the RosettaCommons Consortium. (2020) (0)
- Accurately positioning functional residues with robotics-inspired computational protein design (2021) (0)
- Title Controlling CRISPR-Cas 9 with ligand-activated and ligand-deactivated sgRNAs (2019) (0)
- Biophysical basis of cellular multi-specificity encoded in a model molecular switch (2020) (0)
- Commercial spin-off companies from the Rosetta community. (2020) (0)
- Multi-input drug-controlled switches of mammalian gene expression based on engineered nuclear hormone receptors (2023) (0)
- Growth in Rosetta PIs and conference attendees. (2020) (0)
- Quantitative mapping of protein-peptide affinity landscapes reveals novel calcineurin inhibitors (2018) (0)
- De novo designed NTF2 fold protein NT-9 (2020) (0)
- De novo designed Rossmann fold protein ROS2_36830 (2020) (0)
- Author response: Altered expression of a quality control protease in E. coli reshapes the in vivo mutational landscape of a model enzyme (2020) (0)
- Crystal structure of leukemia inhibitory factor in complex with gp130 (2003) (0)
- Crystal structure of the computationally designed NNOS-Syntrophin complex (2013) (0)
- Cellular Consequences of Systematic Perturbations of a Highly Conserved Biological Switch (2018) (0)
- Emerging maps of allosteric regulation in cellular networks (2023) (0)
- Prediction and Design of Molecular Recognition (2006) (0)
- De novo designed Rossmann fold protein ROS2_49223 (2020) (0)
- Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps (2023) (0)
- Author response: Quantitative mapping of protein-peptide affinity landscapes using spectrally encoded beads (2018) (0)
- PUBS 2018 Biophysics 205 A : Physical Underpinnings of Biological Systems Fall 2018 Syllabus (2018) (0)
- Descriptions of the Rosetta board positions. (2020) (0)
- Paper alert: Structural biology (2001) (0)
- Design of selective and multi‐specific protein‐protein interfaces (2008) (0)
- Ketosteroid isomerase (C. testosteroni) with truncated & designed loop for precise positioning of a catalytic E38 (2020) (0)
- De novo designed Rossmann fold protein ROS2_835 (2020) (0)
- Crystal Structure of the free human NKG2D immunoreceptor (2003) (0)
- Typical development workflow in the Rosetta community. (2020) (0)
- Crystal Structure of catalytic domain of Son of sevenless (Rem-Cdc25) in the absence of Ras (2006) (0)
- Details of Remaining Collective Challenges. (2020) (0)
- Molecular and cellular constraints on proteins (2016) (0)
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What Schools Are Affiliated With Tanja Kortemme?
Tanja Kortemme is affiliated with the following schools:
