James Fraser

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Usage

Usage

Usage is calculated on the last day of every month. For more information on usage data, visit the Usage Overview page.

Table 1: Overview
Item Value
Contributions: 111
Rank by Contributions: 2 / 162
First Contribution: 18 Feb 2013
Last Contribution: 28 May 2025
Citations on Contributions: -
Table 2: Simulation Tool Usage
# Tool Name Users served in last 12 months Simulation Runs in last 12 months Total users served Total Simulation Runs Citations Published On
No data found.
Table 3: "and more" Usage
# Resource Title Users served in last 12 months Total users served Citations Published On
1 Exploration of structure-activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment linking and active learning BioXFEL Publications - - - 28 May 2025
2 Where and how to house big data on small fragments BioXFEL Publications - - - 05 May 2025
3 Advances in uncovering the mechanisms of macromolecular conformational entropy BioXFEL Publications - - - 24 Apr 2025
4 Improving Cryo-EM Experimental Data Fit with Automated Multiconformer Modeling for Proteins and Non-proteins BioXFEL Publications - - - 10 Apr 2025
5 BPS2025 - Unraveling the catalytic mechanism of the SARS-CoV-2 macrodomain ADP-ribosylhydrolase BioXFEL Publications - - - 13 Feb 2025
6 The impact of library size and scale of testing on virtual screening BioXFEL Publications - - - 03 Jan 2025
7 Conserved regulatory motifs in the juxtamembrane domain and kinase N-lobe revealed through deep mutational scanning of the MET receptor tyrosine kinase domain BioXFEL Publications - - - 13 Sep 2024
8 Comprehensive encoding of conformational and compositional protein structural ensembles through the mmCIF data structure BioXFEL Publications - - - 01 Jul 2024
9 Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase BioXFEL Publications - - - 17 Jun 2024
10 Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase BioXFEL Publications - - - 17 Jun 2024
11 Rosace: a robust deep mutational scanning analysis framework employing position and mean-variance shrinkage BioXFEL Publications - - - 24 May 2024
12 Rosace: a robust deep mutational scanning analysis framework employing position and mean-variance shrinkage BioXFEL Publications - - - 24 May 2024
13 Role of conformational dynamics in the catalytic mechanism of viral macrodomains BioXFEL Publications - - - 08 Feb 2024
14 Product-stabilized filamentation by human glutamine synthetase allosterically tunes activity BioXFEL Publications - - - 08 Feb 2024
15 Computing a Bayesian multi-state model of a protein structure from an X-ray diffraction pattern BioXFEL Publications - - - 08 Feb 2024
16 Extracting conformational heterogeneity from 2D and 3D cryo-EM data BioXFEL Publications - - - 08 Feb 2024
17 Discovery and Clinical Proof-of-Concept of RLY-2608, a First-in-Class Mutant-Selective Allosteric PI3Kα Inhibitor That Decouples Antitumor Activity from Hyperinsulinemia BioXFEL Publications - - - 02 Nov 2023
18 Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography BioXFEL Publications - - - 18 Sep 2023
19 A type 2 immune circuit in the stomach controls mammalian adaptation to dietary chitin BioXFEL Publications - - - 07 Sep 2023
20 A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication in vivo BioXFEL Publications - - - 31 Aug 2023
21 Refinement of multiconformer ensemble models from multi-temperature X-ray diffraction data BioXFEL Publications - - - 27 Jul 2023
22 DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology BioXFEL Publications - - - 24 Feb 2023
23 Reaction coordinate dependent fibrillar formation of human glutamine synthetase tunes activity BioXFEL Publications - - - 10 Feb 2023
24 Large language models generate functional protein sequences across diverse families BioXFEL Publications - - - 26 Jan 2023
25 Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2 BioXFEL Publications - - - 04 Jan 2023
26 A language model beats alphafold2 on orphans BioXFEL Publications - - - 03 Oct 2022
27 The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature BioXFEL Publications - - - 27 May 2022
28 Ligand binding remodels protein side-chain conformational heterogeneity BioXFEL Publications - - - 21 Mar 2022
29 Accurate positioning of functional residues with robotics-inspired computational protein design BioXFEL Publications - - - 07 Mar 2022
30 Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics BioXFEL Publications - - - 14 Feb 2022
31 Curiosity: a tool for exploring density features in crystallographic and cryoEM maps BioXFEL Publications - - - 11 Feb 2022
32 Deconvoluting receptor trafficking, regulation, and function using massively parallel assays BioXFEL Publications - - - 11 Feb 2022
33 Integration of software tools for integrative modeling of biomolecular systems BioXFEL Publications - - - 11 Feb 2022
34 Dismantling antibiotic resistance one variant at a time: in vitro and computational analysis of VatD BioXFEL Publications - - - 11 Feb 2022
35 Connecting glutamine synthetase biophysics to the cellular environment BioXFEL Publications - - - 11 Feb 2022
36 Using deep mutational scanning to identify the determinants of antibiotic resistance BioXFEL Publications - - - 11 Feb 2022
37 Integration of software tools for integrative modeling of biomolecular systems BioXFEL Publications - - - 09 Feb 2022
38 Innate Type 2 Immunity Controls Hair Follicle Commensalism by <i>Demodex</i> Mites BioXFEL Publications - - - 22 Jan 2022
39 Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance BioXFEL Publications - - - 11 Jan 2022
40 A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis BioXFEL Publications - - - 20 Dec 2021
41 Turning up the heat on molecular machines with multi-temperature and temperature-jump X-ray scattering experiments BioXFEL Publications - - - 21 Oct 2021
42 Dan Salah Tawfik (1955‐2021)—A giant of protein evolution BioXFEL Publications - - - 28 May 2021
43 State of the structure address on MET receptor activation by HGF BioXFEL Publications - - - 17 Apr 2021
44 ORACLE reveals a bright future to fight bacteria BioXFEL Publications - - - 15 Apr 2021
45 Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking BioXFEL Publications - - - 14 Apr 2021
46 Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge BioXFEL Publications - - - 04 Feb 2021
47 Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray–derived conformational ensembles BioXFEL Publications - - - 23 Dec 2020
48 Genetic interaction mapping informs integrative structure determination of protein complexes BioXFEL Publications - - - 10 Dec 2020
49 qFit 3: Protein and ligand multiconformer modeling for X‐ray crystallographic and single‐particle cryo‐EM density maps BioXFEL Publications - - - 19 Nov 2020
50 Discovery of allosteric binding sites by crystallographic fragment screening BioXFEL Publications - - - 07 Nov 2020
51 Expanding the space of protein geometries by computational design of de novo fold families BioXFEL Publications - - - 16 Oct 2020
52 Synthetic group A streptogramin antibiotics that overcome Vat resistance BioXFEL Publications - - - 23 Sep 2020
53 Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico BioXFEL Publications - - - 23 Sep 2020
54 Targeted DNA sequencing analysis to reveal genetic diversity and androgen-receptor alteration in advanced EGFR mutant lung adenocarcinoma. BioXFEL Publications - - - 25 May 2020
55 A SARS-CoV-2 protein interaction map reveals targets for drug repurposing BioXFEL Publications - - - 30 Apr 2020
56 Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals BioXFEL Publications - - - 25 Feb 2020
57 Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit BioXFEL Publications - - - 14 Jan 2020
58 Differences in the chitinolytic activity of mammalian chitinases on soluble and insoluble substrates BioXFEL Publications - - - 13 Jan 2020
59 Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein BioXFEL Publications - - - 18 Dec 2019
60 Computational design of a modular protein sense-response system BioXFEL Publications - - - 26 Nov 2019
61 Co-occurring Alterations in the RAS–MAPK Pathway Limit Response to MET Inhibitor Treatment in MET Exon 14 Skipping Mutation-Positive Lung Cancer BioXFEL Publications - - - 23 Sep 2019
62 Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme BioXFEL Publications - - - 16 Sep 2019
63 Cysteine modification can gate non-equilibrium conformational dynamics during enzyme catalysis: Supplemental Information BioXFEL Publications - - - 19 Jan 2019
64 Biophysical Characterization of a Disabled Double Mutant of Soybean Lipoxygenase: The “Undoing” of Precise Substrate Positioning Relative to Metal Cofactor and an Identified Dynamical Network BioXFEL Publications - - - 15 Jan 2019
65 Temperature-Jump Solution X-ray Scattering Reveals Distinct Motions in a Dynamic Enzyme: BioXFEL Publications - - - 22 Nov 2018
66 qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps BioXFEL Publications - - - 20 Nov 2018
67 An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering BioXFEL Publications - - - 06 Jun 2018
68 Rescue of conformational dynamics in enzyme catalysis by directed evolution BioXFEL Publications - - - 04 Apr 2018
69 Bringing diffuse X-ray scattering into focus BioXFEL Publications - - - 16 Feb 2018
70 qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps BioXFEL Publications - - - 26 Jan 2018
71 XFEL structures of the influenza M2 proton channel at 1.4 Å: room-temperature water networks and insights into proton conduction BioXFEL Publications - - - 19 Dec 2017
72 New routes for PTP1B allosteric inhibition by multitemperature crystallography, fragment screening and covalent tethering BioXFEL Publications - - - 14 Nov 2017
73 Rescue of Conformational Dynamics in Enzyme Catalysis by Directed Evolution BioXFEL Publications - - - 06 Sep 2017
74 XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction BioXFEL Publications - - - 24 Aug 2017
75 Allosteric Inhibitors, Crystallography, and Comparative Analysis Reveal Network of Coordinated Movement across Human Herpesvirus Proteases BioXFEL Publications - - - 31 Jul 2017
76 A multi-model approach to assessing local and global cryo-EM map quality BioXFEL Publications - - - 20 Apr 2017
77 Flexibility and Design: Conformational Heterogeneity along the Evolutionary Trajectory of a Redesigned Ubiquitin BioXFEL Publications - - - 13 Apr 2017
78 Model Comparison to Identify Structural Heterogeneity in Protein X-Ray Crystallography BioXFEL Publications - - - 04 Feb 2017
79 Cytidine deaminase efficiency of the lentiviral viral restriction factor APOBEC3C correlates with dimerization BioXFEL Publications - - - 30 Jan 2017
80 Conformational variation of proteins at room temperature is not dominated by radiation damage BioXFEL Publications - - - 21 Dec 2016
81 Flexibility and design: conformational heterogeneity along the evolutionary trajectory of a redesigned ubiquitin BioXFEL Publications - - - 19 Oct 2016
82 Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta BioXFEL Publications - - - 27 Apr 2016
83 Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting BioXFEL Publications - - - 25 Apr 2016
84 Measuring and modeling diffuse scattering in protein X-ray crystallography BioXFEL Publications - - - 29 Mar 2016
85 Data publication with the structural biology data grid supports live analysis BioXFEL Publications - - - 07 Mar 2016
86 CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites BioXFEL Publications - - - 05 Feb 2016
87 Measuring and modeling diffuse scattering in protein X-ray crystallography BioXFEL Publications - - - 07 Dec 2015
88 Multitemperature data and diffuse scattering in X-ray crystallography Teaching Materials - - - 07 Dec 2015
89 High-density grids for efficient data collection from multiple crystals BioXFEL Publications - - - 03 Dec 2015
90 High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction BioXFEL Publications - - - 03 Nov 2015
91 Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit BioXFEL Publications - - - 27 Oct 2015
92 Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography BioXFEL Publications - - - 30 Sep 2015
93 Determination of Ubiquitin Fitness Landscapes Under Different Chemical Stresses in a Classroom Setting BioXFEL Publications - - - 26 Aug 2015
94 EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy BioXFEL Publications - - - 17 Aug 2015
95 From deep TLS validation to ensembles of atomic models built from elemental motions BioXFEL Publications - - - 27 Jul 2015
96 Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles BioXFEL Publications - - - 27 Jul 2015
97 Inside Cover: One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites (ChemBioChem 11/2015) BioXFEL Publications - - - 20 Jul 2015
98 One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites BioXFEL Publications - - - 28 May 2015
99 Negative Epistasis and Evolvability in TEM-1 β-Lactamase—The Thin Line between an Enzyme's Conformational Freedom and Disorder BioXFEL Publications - - - 22 May 2015
100 Exposing hidden alternative backbone conformations in X-ray crystallography using qFit BioXFEL Publications - - - 05 May 2015
101 Diffuse X-Ray Scattering for Ensemble Modeling of Crystalline Proteins BioXFEL Publications - - - 18 Apr 2015
102 Integrative, dynamic structural biology at atomic resolution—it's about time BioXFEL Publications - - - 31 Mar 2015
103 Mapping the Conformational Landscape of a Dynamic Enzyme by XFEL and Multitemperature Crystallography BioXFEL Publications - - - 20 Mar 2015
104 Side-chain-directed model and map validation for 3D Electron Cryomicroscopy BioXFEL Publications - - - 09 Feb 2015
105 Predicting X-ray Diffuse Scattering from Translation Libration Screw Structural Ensembles BioXFEL Publications - - - 03 Jan 2015
106 From deep TLS validation to ensembles of atomic models built from elemental motions BioXFEL Publications - - - 03 Jan 2015
107 Keep on Moving: Discovering and Perturbing the Conformational Dynamics of Enzymes BioXFEL Publications - - - 24 Dec 2014
108 E pluribus unum, no more: from one crystal, many conformations BioXFEL Publications - - - 09 Aug 2014
109 Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery BioXFEL Publications - - - 25 May 2014
110 Automated identification of functional dynamic contact networks from X-ray crystallography BioXFEL Publications - - - 05 Aug 2013
111 Flexible Backbone Sampling Methods to Model and Design Protein Alternative Conformations BioXFEL Publications - - - 18 Feb 2013