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Author: James Fraser

Rankings

  • All-time downloads: 219,648 (rank: 438 )
  • Categories:
    • biochemistry: 8,205 (rank: 333 )
    • bioengineering: 1,853 (rank: 2,269 (tie) )
    • bioinformatics: 633 (rank: 26,755 (tie) )
    • biophysics: 24,148 (rank: 29 )
    • cancer biology: 1,437 (rank: 7,233 (tie) )
    • immunology: 455 (rank: 27,172 (tie) )
    • synthetic biology: 3,474 (rank: 478 (tie) )
    • systems biology: 179,443 (rank: 15 )

Downloads per author, site-wide

Preprints

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

systems biology more details view paper
  • Downloaded 178,503 times
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    • Site-wide: 30
    • In systems biology: 1
  • Year to date:
    • Site-wide: 1,563
  • Since beginning of last month:
    • Site-wide: 1,083

Deep neural language modeling enables functional protein generation across families

synthetic biology more details view paper
  • Downloaded 3,474 times
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    • Site-wide: 4,687
    • In synthetic biology: 42
  • Year to date:
    • Site-wide: 1,247
  • Since beginning of last month:
    • Site-wide: 2,976

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

biophysics more details view paper
  • Downloaded 2,951 times
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    • Site-wide: 5,922
    • In biophysics: 92
  • Year to date:
    • Site-wide: 2,493
  • Since beginning of last month:
    • Site-wide: 3,650

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

biophysics more details view paper
  • Downloaded 2,082 times
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    • Site-wide: 9,796
    • In biophysics: 190
  • Year to date:
    • Site-wide: 102,407
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    • Site-wide: 40,652

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

biophysics more details view paper
  • Downloaded 1,799 times
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    • Site-wide: 12,207
    • In biophysics: 267
  • Year to date:
    • Site-wide: 28,448
  • Since beginning of last month:
    • Site-wide: 70,655

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

biochemistry more details view paper
  • Downloaded 1,748 times
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    • Site-wide: 12,730
    • In biochemistry: 254
  • Year to date:
    • Site-wide: 12,173
  • Since beginning of last month:
    • Site-wide: 20,182

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

cancer biology more details view paper
  • Downloaded 1,437 times
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    • Site-wide: 17,187
    • In cancer biology: 371
  • Year to date:
    • Site-wide: 136,696
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    • Site-wide: 96,012

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

biochemistry more details view paper
  • Downloaded 1,271 times
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    • Site-wide: 20,666
    • In biochemistry: 434
  • Year to date:
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    • Site-wide: 118,796

Computational design of a modular protein sense/response system

biophysics more details view paper
  • Downloaded 1,221 times
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    • Site-wide: 21,978
    • In biophysics: 561
  • Year to date:
    • Site-wide: 81,141
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    • Site-wide: 146,837

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

biophysics more details view paper
  • Downloaded 1,215 times
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    • Site-wide: 22,151
    • In biophysics: 565
  • Year to date:
    • Site-wide: 150,121
  • Since beginning of last month:
    • Site-wide: 150,830

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

biophysics more details view paper
  • Downloaded 1,180 times
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    • Site-wide: 23,168
    • In biophysics: 609
  • Year to date:
    • Site-wide: 103,626
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    • Site-wide: 100,172

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

biochemistry more details view paper
  • Downloaded 1,168 times
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    • Site-wide: 23,506
    • In biochemistry: 525
  • Year to date:
    • Site-wide: 70,657
  • Since beginning of last month:
    • Site-wide: 70,696

Effects of α-tubulin acetylation on microtubule structure and stability

biophysics more details view paper
  • Downloaded 1,129 times
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    • Site-wide: 24,788
    • In biophysics: 666
  • Year to date:
    • Site-wide: 104,197
  • Since beginning of last month:
    • Site-wide: 123,907

Measuring and modeling diffuse scattering in protein X-ray crystallography

biophysics more details view paper
  • Downloaded 1,106 times
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    • Site-wide: 25,546
    • In biophysics: 698
  • Year to date:
    • Site-wide: 149,596
  • Since beginning of last month:
    • Site-wide: 62,476

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

biochemistry more details view paper
  • Downloaded 1,081 times
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    • Site-wide: 26,494
    • In biochemistry: 595
  • Year to date:
    • Site-wide: 56,276
  • Since beginning of last month:
    • Site-wide: 81,039

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

biophysics more details view paper
  • Downloaded 1,074 times
  • Download rankings, all-time:
    • Site-wide: 26,742
    • In biophysics: 743
  • Year to date:
    • Site-wide: 145,423
  • Since beginning of last month:
    • Site-wide: 109,046

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

biophysics more details view paper
  • Downloaded 1,035 times
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    • Site-wide: 28,248
    • In biophysics: 796
  • Year to date:
    • Site-wide: 102,466
  • Since beginning of last month:
    • Site-wide: 51,737

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

bioengineering more details view paper
  • Downloaded 1,026 times
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    • Site-wide: 28,562
    • In bioengineering: 511
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 90,809

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

biochemistry more details view paper
  • Downloaded 956 times
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    • Site-wide: 31,723
    • In biochemistry: 760
  • Year to date:
    • Site-wide: 128,722
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    • Site-wide: 55,359

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

systems biology more details view paper
  • Downloaded 940 times
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    • Site-wide: 32,546
    • In systems biology: 643
  • Year to date:
    • Site-wide: 54,558
  • Since beginning of last month:
    • Site-wide: 122,109

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

biophysics more details view paper
  • Downloaded 919 times
  • Download rankings, all-time:
    • Site-wide: 33,664
    • In biophysics: 1,009
  • Year to date:
    • Site-wide: 16,022
  • Since beginning of last month:
    • Site-wide: 80,649

Accurately positioning functional residues with robotics-inspired computational protein design

bioengineering more details view paper
  • Downloaded 827 times
  • Download rankings, all-time:
    • Site-wide: 39,281
    • In bioengineering: 747
  • Year to date:
    • Site-wide: 51,745
  • Since beginning of last month:
    • Site-wide: 3,111

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

biophysics more details view paper
  • Downloaded 809 times
  • Download rankings, all-time:
    • Site-wide: 40,497
    • In biophysics: 1,259
  • Year to date:
    • Site-wide: 102,465
  • Since beginning of last month:
    • Site-wide: 99,436

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

biophysics more details view paper
  • Downloaded 800 times
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    • Site-wide: 41,170
    • In biophysics: 1,287
  • Year to date:
    • Site-wide: 89,011
  • Since beginning of last month:
    • Site-wide: 58,086

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

biophysics more details view paper
  • Downloaded 795 times
  • Download rankings, all-time:
    • Site-wide: 41,541
    • In biophysics: 1,303
  • Year to date:
    • Site-wide: 107,963
  • Since beginning of last month:
    • Site-wide: 129,388

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

biophysics more details view paper
  • Downloaded 790 times
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    • Site-wide: 41,885
    • In biophysics: 1,321
  • Year to date:
    • Site-wide: 149,547
  • Since beginning of last month:
    • Site-wide: 80,722

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

biophysics more details view paper
  • Downloaded 773 times
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    • Site-wide: 43,207
    • In biophysics: 1,383
  • Year to date:
    • Site-wide: 102,436
  • Since beginning of last month:
    • Site-wide: 160,867

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

biochemistry more details view paper
  • Downloaded 724 times
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    • Site-wide: 47,445
    • In biochemistry: 1,216
  • Year to date:
    • Site-wide: 10,017
  • Since beginning of last month:
    • Site-wide: 20,432

Bringing Diffuse X-ray Scattering Into Focus

biophysics more details view paper
  • Downloaded 720 times
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    • Site-wide: 47,824
    • In biophysics: 1,553
  • Year to date:
    • Site-wide: 57,028
  • Since beginning of last month:
    • Site-wide: 150,820

Rescue of Conformational Dynamics in Enzyme Catalysis by Directed Evolution

biophysics more details view paper
  • Downloaded 712 times
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    • Site-wide: 48,526
    • In biophysics: 1,578
  • Year to date:
    • Site-wide: 76,722
  • Since beginning of last month:
    • Site-wide: 122,225

Model selection for biological crystallography

biophysics more details view paper
  • Downloaded 692 times
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    • Site-wide: 50,528
    • In biophysics: 1,648
  • Year to date:
    • Site-wide: 146,922
  • Since beginning of last month:
    • Site-wide: 105,800

A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis

biochemistry more details view paper
  • Downloaded 638 times
  • Download rankings, all-time:
    • Site-wide: 56,348
    • In biochemistry: 1,488
  • Year to date:
    • Site-wide: 14,186
  • Since beginning of last month:
    • Site-wide: 12,493

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

bioinformatics more details view paper
  • Downloaded 633 times
  • Download rankings, all-time:
    • Site-wide: 56,898
    • In bioinformatics: 5,615
  • Year to date:
    • Site-wide: 97,053
  • Since beginning of last month:
    • Site-wide: 152,874

Ligand binding remodels protein side chain conformational heterogeneity

biophysics more details view paper
  • Downloaded 554 times
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    • Site-wide: 67,441
    • In biophysics: 2,344
  • Year to date:
    • Site-wide: 50,713
  • Since beginning of last month:
    • Site-wide: 22,893

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

biochemistry more details view paper
  • Downloaded 535 times
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    • Site-wide: 70,224
    • In biochemistry: 1,890
  • Year to date:
    • Site-wide: 35,308
  • Since beginning of last month:
    • Site-wide: 109,945

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

biophysics more details view paper
  • Downloaded 511 times
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    • Site-wide: 74,012
    • In biophysics: 2,631
  • Year to date:
    • Site-wide: 5,694
  • Since beginning of last month:
    • Site-wide: 18,466

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

biophysics more details view paper
  • Downloaded 487 times
  • Download rankings, all-time:
    • Site-wide: 78,308
    • In biophysics: 2,815
  • Year to date:
    • Site-wide: 58,554
  • Since beginning of last month:
    • Site-wide: 108,950

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

immunology more details view paper
  • Downloaded 455 times
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    • Site-wide: 84,207
    • In immunology: 2,580
  • Year to date:
    • Site-wide: 21,948
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    • Site-wide: 59,087

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

biophysics more details view paper
  • Downloaded 451 times
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    • Site-wide: 85,159
    • In biophysics: 3,120
  • Year to date:
    • Site-wide: 102,467
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    • Site-wide: 122,302

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

biophysics more details view paper
  • Downloaded 343 times
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    • Site-wide: 109,653
    • In biophysics: 4,176
  • Year to date:
    • Site-wide: 137,721
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    • Site-wide: 132,745

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

biochemistry more details view paper
  • Downloaded 84 times
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    • Site-wide: 168,415
    • In biochemistry: 5,145
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