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A Pareto-optimal refinement method for protein design scaffolds

PloS one, 2013-04, Vol.8 (4), p.e59004-e59004

2013

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Computational Enzyme Design

Angewandte Chemie (International ed.), 2013-05, Vol.52 (22), p.5700-5725

International ed. in English, 2013

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Engineering an allosteric transcription factor to respond to new ligands

Nature methods, 2016-02, Vol.13 (2), p.177-183

2016

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Scoring functions for protein–protein interactions

Current opinion in structural biology, 2013-12, Vol.23 (6), p.862-867

2013

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Rosetta FlexPepDock to predict peptide-MHC binding: An approach for non-canonical amino acids

PloS one, 2022-12, Vol.17 (12), p.e0275759

2022

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Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins

PLoS computational biology, 2024-03, Vol.20 (3), p.e1011939-e1011939

2024

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

PLoS computational biology, 2020-05, Vol.16 (5), p.e1007507

2020

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Rearrangement of the Extracellular Domain/Extracellular Loop 1 Interface Is Critical for Thyrotropin Receptor Activation

The Journal of biological chemistry, 2016-07, Vol.291 (27), p.14095-14108

2016

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Enhancing the Latent Nucleotide Triphosphate Flexibility of the Glucose-1-phosphate Thymidylyltransferase RmlA

The Journal of biological chemistry, 2007-06, Vol.282 (23), p.16942-16947

2007

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Expanding the Nucleotide and Sugar 1-Phosphate Promiscuity of Nucleotidyltransferase RmlA via Directed Evolution

The Journal of biological chemistry, 2011-04, Vol.286 (15), p.13235-13243

2011

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Delineating the Molecular Basis of the Calmodulin‒bMunc13-2 Interaction by Cross-Linking/Mass Spectrometry-Evidence for a Novel CaM Binding Motif in bMunc13-2

Cells (Basel, Switzerland), 2020-01, Vol.9 (1), p.136

2020

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in vitro Characterization of Polyene Glycosyltransferases AmphDI and NysDI

Chembiochem : a European journal of chemical biology, 2008-10, Vol.9 (15), p.2506-2514

2008

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Targeted Chemical Wedges Reveal the Role of Allosteric DNA Modulation in Protein−DNA Assembly

ACS chemical biology, 2008-04, Vol.3 (4), p.220-229

2008

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Web‐accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE)

Protein science, 2018-01, Vol.27 (1), p.259-268

2018

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Protocols for Molecular Modeling with Rosetta3 and RosettaScripts

Biochemistry (Easton), 2016-08, Vol.55 (34), p.4748-4763

2016

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Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1

Proceedings of the National Academy of Sciences - PNAS, 2021-03, Vol.118 (12)

2021

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Mono(2‐ethylhexyl) phthalate (MEHP) and mono(2‐ethyl‐5‐oxohexyl) phthalate (MEOHP) but not di(2‐ethylhexyl) phthalate (DEHP) bind productively to the peroxisome proliferator‐activated receptor γ

Rapid communications in mass spectrometry, 2019-05, Vol.33 (S1), p.75-85

2019

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Rosetta and the Design of Ligand Binding Sites

Methods in molecular biology (Clifton, N.J.), 2016-01, Vol.1414, p.47

2016

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Temperature-Sensitive Protein-DNA Dimerizers

Proceedings of the National Academy of Sciences - PNAS, 2005-04, Vol.102 (14), p.5008-5013

2005

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A comparison of sugar indicators enables a universal high-throughput sugar-1-phosphate nucleotidyltransferase assay

Analytical biochemistry, 2008-06, Vol.377 (2), p.251-258

2008

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Identification of a ubiquitin-binding interface using Rosetta and DEER

Proceedings of the National Academy of Sciences - PNAS, 2018-01, Vol.115 (3), p.525-530

2018

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Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

Biochemistry (Easton), 2021-03, Vol.60 (11), p.825-846

2021

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

Nature communications, 2021-11, Vol.12 (1), p.6947-6947, Article 6947

2021

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

Proteins, structure, function, and bioinformatics, 2013-11, Vol.81 (11), p.1980-1987

2013

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Expanding the specificity of DNA targeting by harnessing cooperative assembly

Biochimie, 2008-07, Vol.90 (7), p.1015-1025

2008

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A Pareto-optimal refinement method for protein design scaffolds

Computational Enzyme Design

Engineering an allosteric transcription factor to respond to new ligands

Scoring functions for protein–protein interactions

Rosetta FlexPepDock to predict peptide-MHC binding: An approach for non-canonical amino acids

Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins

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

Rearrangement of the Extracellular Domain/Extracellular Loop 1 Interface Is Critical for Thyrotropin Receptor Activation

Enhancing the Latent Nucleotide Triphosphate Flexibility of the Glucose-1-phosphate Thymidylyltransferase RmlA

Expanding the Nucleotide and Sugar 1-Phosphate Promiscuity of Nucleotidyltransferase RmlA via Directed Evolution

Delineating the Molecular Basis of the Calmodulin‒bMunc13-2 Interaction by Cross-Linking/Mass Spectrometry-Evidence for a Novel CaM Binding Motif in bMunc13-2

in vitro Characterization of Polyene Glycosyltransferases AmphDI and NysDI

Targeted Chemical Wedges Reveal the Role of Allosteric DNA Modulation in Protein−DNA Assembly

Web‐accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE)

Protocols for Molecular Modeling with Rosetta3 and RosettaScripts

Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1

Mono(2‐ethylhexyl) phthalate (MEHP) and mono(2‐ethyl‐5‐oxohexyl) phthalate (MEOHP) but not di(2‐ethylhexyl) phthalate (DEHP) bind productively to the peroxisome proliferator‐activated receptor γ

Rosetta and the Design of Ligand Binding Sites

Temperature-Sensitive Protein-DNA Dimerizers

A comparison of sugar indicators enables a universal high-throughput sugar-1-phosphate nucleotidyltransferase assay

Identification of a ubiquitin-binding interface using Rosetta and DEER

Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

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

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

Expanding the specificity of DNA targeting by harnessing cooperative assembly

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