Author: James S. Fraser

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Preprints

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

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Deep neural language modeling enables functional protein generation across families

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CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.

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A multi-model approach to assessing local and global cryo-EM map quality

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Mapping the Conformational Landscape of a Dynamic Enzyme by XFEL and Multitemperature Crystallography

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Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking

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Co-occurring alterations in the RAS-MAPK pathway limit response to MET inhibitor treatment in MET exon 14 skipping mutation positive lung cancer

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Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta

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Computational design of a modular protein sense/response system

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qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps

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Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis

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Temperature-Jump Solution X-ray Scattering Reveals Distinct Motions in a Dynamic Enzyme

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Effects of α-tubulin acetylation on microtubule structure and stability

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High-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit and validation of nucleotide modifications

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Measuring and modeling diffuse scattering in protein X-ray crystallography

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Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

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Side-chain-directed model and map validation for 3D Electron Cryomicroscopy

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

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Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution

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Accurately positioning functional residues with robotics-inspired computational protein design

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New routes for PTP1B allosteric inhibition by multitemperature crystallography, fragment screening and covalent tethering

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Determination of Ubiquitin Fitness Landscapes Under Different Chemical Stresses in a Classroom Setting

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Evolution of an enzyme conformational ensemble guides design of an efficient biocatalyst

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Exposing hidden alternative backbone conformations in X-ray crystallography using qFit

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Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray-derived conformational ensembles

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Predicting X-ray Diffuse Scattering from Translation Libration Screw Structural Ensembles

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Flexibility and design: conformational heterogeneity along the evolutionary trajectory of a redesigned ubiquitin

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Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance

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  • In biochemistry: 1,220
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Bringing Diffuse X-ray Scattering Into Focus

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Rescue of Conformational Dynamics in Enzyme Catalysis by Directed Evolution

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A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis

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Model selection for biological crystallography

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Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics

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Ligand binding remodels protein side chain conformational heterogeneity

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Extending Chemical Perturbations Of The Ubiquitin Fitness Landscape In A Classroom Setting

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Differences in the chitinolytic activity of mammalian chitinases on soluble and crystalline substrates

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qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps

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Type 2 innate immunity regulates hair follicle homeostasis to control Demodex pathosymbionts

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  • In immunology: 2,565
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The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and X-ray diffraction at room temperature

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From deep TLS validation to ensembles of atomic models built from elemental motions

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Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein

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Molecular-Dynamics Simulation Methods for Macromolecular Crystallography

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Ensemble-function relationships to evaluate catalysis in the ketosteroid isomerase oxyanion hole

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