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Author Details

Tanja Kortemme
University of California san francisco
1993
114
59
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36801015A complete allosteric map of a GTPase switch in its native cellular network.Cell Syst2023
37452025Author Correction: Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor.Nat Commun2023
37315218Multi-input Drug-Controlled Switches of Mammalian Gene Expression Based on Engineered Nuclear Hormone Receptors.ACS Synth Biol2023
37150039Emerging maps of allosteric regulation in cellular networks.Curr Opin Struct Biol2023
36859492Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor.Nat Commun2023
36778233Multi-input drug-controlled switches of mammalian gene expression based on engineered nuclear hormone receptors.bioRxiv2023
36805129Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps.Structure2023
34537489Design principles of protein switches.Curr Opin Struct Biol2022
35667008Correction to "The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design".J Chem Theory Comput2022
36531560Advances in the Computational Design of Small-Molecule-Controlled Protein-Based Circuits for Synthetic Biology.Proc IEEE Inst Electr Electron Eng2022
35982665Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps.bioRxiv2022
35254891Accurate positioning of functional residues with robotics-inspired computational protein design.Proc Natl Acad Sci U S A2022
34031651CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.Res Sq2021
33744284Recent advances in de novo protein design: Principles, methods, and applications.J Biol Chem2021
33833059Reply to Liu et al.: Specific mutations matter in specificity and catalysis in ACE2.Proc Natl Acad Sci U S A2021
34646016Systems-level effects of allosteric perturbations to a model molecular switch.Nature2021
34807909De novo protein fold families expand the designable ligand binding site space.PLoS Comput Biol2021
34013269CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.bioRxiv2021
31344278Comparison of Rosetta flexible-backbone computational protein design methods on binding interactions.Proteins2020
33060197Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.Science2020
33093202Engineered ACE2 receptor traps potently neutralize SARS-CoV-2.Proc Natl Acad Sci U S A2020
32855341Expanding the space of protein geometries by computational design of de novo fold families.Science2020
32766586Engineered ACE2 receptor traps potently neutralize SARS-CoV-2.bioRxiv2020
33017412New computational protein design methods for de novo small molecule binding sites.PLoS Comput Biol2020
32701056Altered expression of a quality control protease in <i>E. coli</i> reshapes the in vivo mutational landscape of a model enzyme.Elife2020
32645325The Global Phosphorylation Landscape of SARS-CoV-2 Infection.Cell2020
32365137Better together: Elements of successful scientific software development in a distributed collaborative community.PLoS Comput Biol2020
32353859A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.Nature2020
32483333Macromolecular modeling and design in Rosetta: recent methods and frameworks.Nat Methods2020
30676995Computational design of structured loops for new protein functions.Biol Chem2019
31754004Computational design of a modular protein sense-response system.Science2019
31073154Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs.Nat Commun2019
29401388Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein-Protein Binding Affinity upon Mutation.J Phys Chem B2018
30037883Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance.Biol Open2018
28686159Deconstruction of the Ras switching cycle through saturation mutagenesis.Elife2017
28430426The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design.J Chem Theory Comput2017
28893998Engineering a light-activated caspase-3 for precise ablation of neurons in vivo.Proc Natl Acad Sci U S A2017
27021162A Model for the Molecular Mechanism of an Engineered Light-Driven Protein Machine.Structure2016
27094293Design of Light-Controlled Protein Conformations and Functions.Methods Mol Biol2016
27111525Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting.Elife2016
25866491Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta.J Chem Theory Comput2015
26335248A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design.PLoS One2015
26397464Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity.PLoS Comput Biol2015
25175941Editorial overview: Engineering and design: raising the bar through innovation and integration.Curr Opin Struct Biol2014
25313039Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition.Proc Natl Acad Sci U S A2014
23159126Design of a phosphorylatable PDZ domain with peptide-specific affinity changes.Structure2013
24270642Reprogramming an ATP-driven protein machine into a light-gated nanocage.Nat Nanotechnol2013
24255821Amino-acid site variability among natural and designed proteins.PeerJ2013
24244128Computational protein design quantifies structural constraints on amino acid covariation.PLoS Comput Biol2013
23923816Design of a photoswitchable cadherin.J Am Chem Soc2013
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Collaborators

David Baker
University of Washington
Co-authored papers 26
James S Fraser
University of California san francisco
Co-authored papers 12
Oren S Rosenberg
University of California san francisco
Co-authored papers 10
Brian Kuhlman
Co-authored papers 9
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Johns Hopkins University
Co-authored papers 9
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Co-authored papers 9
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Co-authored papers 7
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Co-authored papers 7
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Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes
Co-authored papers 7
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J. David Gladstone Institutes
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Richard Bonneau
Center for Computational Biology (CCB), Flatiron Institute, Simons Foundation
Co-authored papers 5
Komal Ishwar Pawar
University of California san francisco
Co-authored papers 5
Amber M Smith
University of California san francisco
Co-authored papers 5
Roland L Dunbrack
Fox Chase Cancer Center
Co-authored papers 5
Axel F Brilot
University of California san francisco
Co-authored papers 5
Fengbo Zhou
Washington University School of Medicine
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Gregory E Merz
University of California san francisco
Co-authored papers 5
Mark J S Kelly
Department of Pharmaceutical Chemistry, University of California San Francisco
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Joseph L DeRisi
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Co-authored papers 4
Robyn M Kaake
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David A Agard
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Co-authored papers 4
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Release 1.2