James S. Fraser

Department of Bioengineering and Therapeutic Sciences, University of California San Francisco.

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 5%percentile

0.375Author DataRank

Indexed papers

1in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 1 indexed paper attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.12.147033

Top 48%

0.375DataRank

Top 48%7 citations

Andriy Kryshtafovych, Paul D. Adams, Pavel V. Afonine, Matthew L. Baker, Benjamin A. Barad +49 more

Papers

Driven by 107 papers — median percentile 52. Top paper: “Preprints for the life sciences”.

Preprints for the life sciences

Science(2016)10.1126/science.aaf9133

N/A

16.5DataRank · unranked

199 citations

Needhi Bhalla, Philip E. Bourne, Martin Chalfie, David G. Drubin, James S. Fraser +20 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.22.002386

N/A

14.3DataRank · unranked

456 citations

Gwendolyn M. Jang, Mehdi Bouhaddou, Jiewei Xu, Kirsten Obernier, Matthew J. O’Meara +95 more

Genetic interaction mapping informs integrative structure determination of protein complexes

Science(2020)10.1126/science.aaz4910

N/A

1.1DataRank · unranked

36 citations

Ignacia Echeverria, Stefan Bohn, Peter Cimermančič, Anthony L. Shiver, Richard Alexander +23 more

Recommendations for accelerating open preprint peer review to improve the culture of science

PLOS Biology(2024)10.1371/journal.pbio.3002502

N/A

0.947DataRank · unranked

23 citations

Frédérique Belliard, Amy Brand, Katherine Brown, Géraldine Clément-Stoneham, Stephanie Dawson +53 more

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

Research Square(2021)10.21203/rs.3.rs-515215/v1

N/A

0.796DataRank · unranked

17 citations

Meghna Gupta, Caleigh M. Azumaya, Michelle Moritz, Sergei Pourmal, Amy Diallo +75 more

Conserved regulatory motifs in the juxtamembrane domain and kinase N-lobe revealed through deep mutational scanning of the MET receptor tyrosine kinase domain

eLife(2023)10.7554/elife.91619

N/A

0.590DataRank · unranked

17 citations

Edmond M. Linossi, Christian B. Macdonald, Carla A. Espinoza, Jennifer M. Michaud, Willow Coyote‐Maestas +4 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.12.147033

Top 48%

0.375DataRank

Top 48%7 citations

Andriy Kryshtafovych, Paul D. Adams, Pavel V. Afonine, Matthew L. Baker, Benjamin A. Barad +49 more

Mapping kinase domain resistance mechanisms for the MET receptor tyrosine kinase via deep mutational scanning

eLife(2025)10.7554/elife.101882.3

N/A

0.269DataRank · unranked

5 citations

Edmond M. Linossi, J. N. K. Rao, Christian B. Macdonald, Ashraya Ravikumar, Karson M Chrispens +7 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.29.437438

N/A

0.104DataRank · unranked

1 citations

Maya E. Kotas, Iliana Tenvooren, Diana M. Marquez, Marlys S. Fassett, Jinwoo Lee +9 more

The Mac1 ADP-ribosylhydrolase is a therapeutic target for SARS-CoV-2

eLife(2025)10.7554/elife.103484.3

N/A

0.104DataRank · unranked

1 citations

Priyadarshini Jaishankar, G.J. Correy, Moira Rachman, Patrick C. O’Leary, Taha Y. Taha +26 more

Targeted DNA sequencing analysis to reveal genetic diversity and androgen-receptor alteration in advanced EGFR mutant lung adenocarcinoma.

Journal of Clinical Oncology(2020)10.1200/jco.2020.38.15_suppl.9526

N/A

0DataRank · unranked

0 citations

Ross A. Okimoto, Collin M. Blakely, James S. Fraser, Trever G. Bivona, Wei Wu

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

Science Advances(2021)10.1126/sciadv.abf8711

N/A

0DataRank · unranked

209 citations

G.J. Correy, Stefan Gahbauer, D. Fearon, Taiasean Wu, Roberto Efraín Díaz +48 more

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

Nature Methods(2021)10.1038/s41592-020-01051-w

N/A

0DataRank · unranked

119 citations

Andriy Kryshtafovych, Paul D. Adams, Pavel V. Afonine, Matthew L. Baker, Benjamin A. Barad +49 more

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

eLife(2021)10.7554/elife.70017

N/A

0DataRank · unranked

27 citations

Vanja Stojković, Lianet Noda‐García, I.D. Young, Alexander G. Myasnikov, Jordan Kleinman +7 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.05.10.443524

N/A

0DataRank · unranked

84 citations

Caleigh M. Azumaya, Michelle Moritz, Sergei Pourmal, Amy Diallo, Gregory E. Merz +75 more

Ligand binding remodels protein side chain conformational heterogeneity

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.21.461269

N/A

0DataRank · unranked

11 citations

Saulo H. P. de Oliveira, Daniel W. Hogan, Henry van den Bedem, James S. Fraser, Stephanie A. Wankowicz

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

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.08.10.455846

N/A

0DataRank · unranked

3 citations

Vanja Stojković, D. John Lee, I.D. Young, Teresa Szal, Nora Vázquez‐Laslop +4 more

Ribosomal RNA methylation by GidB modulates discrimination of mischarged tRNA

eLife(2021)10.1101/2021.03.02.433644

N/A

0DataRank · unranked

2 citations

Yuxiang Chen, I.D. Young, Hong-Wei Su, Yuemeng Chen, Jia-Yao Hong +3 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.12.435202

N/A

0DataRank · unranked

2 citations

Vanja Stojković, Lianet Noda‐García, I.D. Young, Alexander Myasnikov, Jordan Kleinman +7 more

A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.12.439528

N/A

0DataRank · unranked

0 citations

D. John Lee, Nadav Elad, Shay Vimer, Michal Sharon, James S. Fraser +2 more

Accurately positioning functional residues with robotics-inspired computational protein design

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.02.450934

N/A

0DataRank · unranked

0 citations

Kale Kundert, Xingjie Pan, Roland A. Pache, Lin Liu, Shane Ó Conchúir +6 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.29.461692

N/A

0DataRank · unranked

0 citations

Tzanko Doukov, Margaux M. Pinney, J.T. Biel, James S. Fraser, Daniel Herschlag +1 more

Ligand binding remodels protein side-chain conformational heterogeneity

eLife(2022)10.7554/elife.74114

N/A

0DataRank · unranked

102 citations

Saulo H de Oliveira, Daniel W Hogan, Henry van den Bedem, James S. Fraser, Stephanie A. Wankowicz

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

Nature Structural & Molecular Biology(2022)10.1038/s41594-022-00723-9

N/A

0DataRank · unranked

69 citations

Vanja Stojković, D. John Lee, I.D. Young, Teresa Szal, Dorota Klepacki +5 more

Ensemble-function relationships to dissect mechanisms of enzyme catalysis

Science Advances(2022)10.1126/sciadv.abn7738

N/A

0DataRank · unranked

58 citations

Tzanko Doukov, Margaux M. Pinney, J.T. Biel, James S. Fraser, Daniel Herschlag +1 more

The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature

Science Advances(2022)10.1126/sciadv.abo5083

N/A

0DataRank · unranked

53 citations

Daniel W. Kneller, G.N. Phillips, Swati Pant, Silvia Russi, Aina E. Cohen +10 more

Innate type 2 immunity controls hair follicle commensalism by Demodex mites

Immunity(2022)10.1016/j.immuni.2022.08.001

N/A

0DataRank · unranked

47 citations

Maya E. Kotas, Claire E. O’Leary, Katelyn Singh, William Damsky, Chang Liao +17 more

Molecular-dynamics simulation methods for macromolecular crystallography

Acta Crystallographica Section D Structural Biology(2022)10.1107/s2059798322011871

N/A

0DataRank · unranked

27 citations

Phillip C. Aoto, Lily Vu, Alexander M. Wolff, David L. Mobley, James S. Fraser +3 more

Integration of software tools for integrative modeling of biomolecular systems

Journal of Structural Biology(2022)10.1016/j.jsb.2022.107841

N/A

0DataRank · unranked

19 citations

Thomas-Otavio Peulen, Benjamin Webb, Billy K. Poon, James S. Fraser, Paul D. Adams +2 more

Accurate positioning of functional residues with robotics-inspired computational protein design

Proceedings of the National Academy of Sciences(2022)10.1073/pnas.2115480119

N/A

0DataRank · unranked

10 citations

Kale Kundert, Xingjie Pan, Roland A. Pache, Lin Liu, Shane Ó Conchúir +6 more

Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 Macrodomain of SARS-CoV-2

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.06.27.497816

N/A

0DataRank · unranked

15 citations

G.J. Correy, M. Schuller, Matteo P. Ferla, Yagmur U. Doruk, Moira Rachman +17 more

Mapping Protein Dynamics at High Spatial Resolution with Temperature-Jump X-ray Crystallography

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.06.10.495662

N/A

0DataRank · unranked

12 citations

Eriko Nango, I.D. Young, Aaron S. Brewster, Minoru Kubo, Takashi Nomura +20 more

Fragment-Based Hit Discovery via Unsupervised Learning of Fragment-Protein Complexes

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.21.517375

N/A

0DataRank · unranked

9 citations

Ivan Ahel, Haim Barr, G.J. Correy, James S. Fraser, Nir London +4 more

The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and X-ray diffraction at room temperature

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.07.479477

N/A

0DataRank · unranked

4 citations

Daniel W. Kneller, G.N. Phillips, Swati Pant, Silvia Russi, Aina E. Cohen +10 more

Molecular-Dynamics Simulation Methods for Macromolecular Crystallography

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.04.486986

N/A

0DataRank · unranked

4 citations

Phillip C. Aoto, Lily Vu, Alexander M. Wolff, David L. Mobley, James S. Fraser +3 more

Molecular evidence of widespread benzimidazole drug resistance in Ancylostoma caninum from domestic dogs throughout the USA and discovery of a novel isotype-1 β-tubulin benzimidazole resistance mutation

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.10.12.511840

N/A

0DataRank · unranked

2 citations

Pablo D. Jimenez Castro, Arianna Morosetti, Hannah Horvath, Rebecca Chen, Elizabeth Redman +7 more

Large language models generate functional protein sequences across diverse families

Nature Biotechnology(2023)10.1038/s41587-022-01618-2

N/A

0DataRank · unranked

1076 citations

Ben Krause, Eric R. Greene, Subu Subramanian, Benjamin P. Mohr, James M. Holton +7 more

Bacteriophages inhibit and evade cGAS-like immune function in bacteria

Cell(2023)10.1016/j.cell.2022.12.041

N/A

0DataRank · unranked

135 citations

Xueli Cao, Jie Ren, Januka S. Athukoralage, Zhaorong Luo, Sukrit Silas +7 more

Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2

Proceedings of the National Academy of Sciences(2023)10.1073/pnas.2212931120

N/A

0DataRank · unranked

132 citations

G.J. Correy, M. Schuller, Matteo P. Ferla, Yagmur U. Doruk, Moira Rachman +17 more

Molecular evidence of widespread benzimidazole drug resistance in Ancylostoma caninum from domestic dogs throughout the USA and discovery of a novel β-tubulin benzimidazole resistance mutation

PLoS Pathogens(2023)10.1371/journal.ppat.1011146

N/A

0DataRank · unranked

94 citations

Pablo D. Jimenez Castro, Arianna Morosetti, Hannah Horvath, Rebecca Chen, Elizabeth Redman +7 more

DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology

Genome biology(2023)10.1186/s13059-023-02880-6

N/A

0DataRank · unranked

76 citations

David Nedrud, Patrick Rockefeller Grimes, Donovan Trinidad, James S. Fraser, Willow Coyote‐Maestas +1 more

Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography

Nature Chemistry(2023)10.1038/s41557-023-01329-4

N/A

0DataRank · unranked

69 citations

Eriko Nango, I.D. Young, Aaron S. Brewster, Minoru Kubo, Takashi Nomura +20 more

A type 2 immune circuit in the stomach controls mammalian adaptation to dietary chitin

Science(2023)10.1126/science.add5649

N/A

0DataRank · unranked

56 citations

Yilin Wang, Haerin Jung, Rachael L. Field, Xinya Zhang, Ta‐Chiang Liu +5 more

A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication in vivo

PLoS Pathogens(2023)10.1371/journal.ppat.1011614

N/A

0DataRank · unranked

37 citations

Rahul K. Suryawanshi, Irene P. Chen, G.J. Correy, Maria McCavitt-Malvido, Patrick C. O’Leary +12 more

Automated multiconformer model building for X-ray crystallography and cryo-EM

eLife(2023)10.7554/elife.90606

N/A

0DataRank · unranked

32 citations

Ashraya Ravikumar, Shivani Sharma, Blake T. Riley, Akshay Raju, Daniel W. Hogan +5 more

Chemoenzymatic Syntheses of Fluorine-18-Labeled Disaccharides from [18F] FDG Yield Potent Sensors of Living Bacteria In Vivo

Journal of the American Chemical Society(2023)10.1021/jacs.3c03338

N/A

0DataRank · unranked

25 citations

Marina López‐Álvarez, Sarah Rabbitt, Aryn A. Alanizi, Rebecca Shuere, Kondapa Naidu Bobba +14 more

Refinement of multiconformer ensemble models from multi-temperature X-ray diffraction data

Methods in enzymology on CD-ROM/Methods in enzymology(2023)10.1016/bs.mie.2023.06.009

N/A

0DataRank · unranked

21 citations

Stephanie A. Wankowicz, Filip Yabukarski, Tzanko Doukov, Daniel Herschlag, James S. Fraser +1 more

Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase

eLife(2023)10.7554/elife.89918

N/A

0DataRank · unranked

5 citations

Andrew K. Ecker, G.J. Correy, Pooja Asthana, I.D. Young, Bryan Faust +6 more

Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.28.546963

N/A

0DataRank · unranked

13 citations

Ashraya Ravikumar, Shivani Sharma, Blake T. Riley, Akshay Raju, Jessica Flowers +5 more

Refinement of Multiconformer Ensemble Models from Multi-temperature X-ray Diffraction Data

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.05.539620

N/A

0DataRank · unranked

7 citations

Stephanie A. Wankowicz, Filip Yabukarski, Tzanko Doukov, Daniel Herschlag, James S. Fraser +1 more

Conserved regulatory motifs in the juxtamembrane domain and kinase N-lobe revealed through deep mutational scanning of the MET receptor tyrosine kinase domain

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.03.551866

N/A

0DataRank · unranked

7 citations

Edmond M. Linossi, Christian B. Macdonald, Carla A. Espinoza, Jennifer M. Michaud, Willow Coyote‐Maestas +4 more

MET variants with activating N-lobe mutations identified in hereditary papillary renal cell carcinomas still require ligand stimulation

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.03.565283

N/A

0DataRank · unranked

6 citations

Audrey Vinchent, Marie Fernandes, Isabelle Damour, Agathe Laratte, Rémi Tellier +10 more

A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication and pathogenesis in vivo

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.18.537104

N/A

0DataRank · unranked

3 citations

Rahul K. Suryawanshi, Irene P. Chen, G.J. Correy, Patrick C. O’Leary, Manasi P. Jogalekar +10 more

Making sense of chaos: uncovering the mechanisms of conformational entropy

ChemRxiv(2023)10.26434/chemrxiv-2023-9b5k7

N/A

0DataRank · unranked

2 citations

James S. Fraser, Stephanie A. Wankowicz

Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM

(2023)10.7554/elife.90606.1

N/A

0DataRank · unranked

1 citations

Ashraya Ravikumar, Shivani Sharma, Blake T. Riley, Akshay Raju, Daniel W. Hogan +4 more

Conserved regulatory motifs in the juxtamembrane domain and kinase N-lobe revealed through deep mutational scanning of the MET receptor tyrosine kinase domain

(2023)10.7554/elife.91619.1

N/A

0DataRank · unranked

1 citations

Edmond M. Linossi, Christian B. Macdonald, Carla A. Espinoza, Jennifer M. Michaud, Willow Coyote‐Maestas +4 more

Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.03.542675

N/A

0DataRank · unranked

0 citations

Andrew K. Ecker, G.J. Correy, Pooja Asthana, I.D. Young, Bryan Faust +6 more

Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase

(2023)10.7554/elife.89918.1

N/A

0DataRank · unranked

0 citations

Andrew K. Ecker, G.J. Correy, Pooja Asthana, I.D. Young, Bryan Faust +6 more

Reviewer #2 (Public Review): Conserved regulatory motifs in the juxtamembrane domain and kinase N-lobe revealed through deep mutational scanning of the MET receptor tyrosine kinase domain

(2023)10.7554/elife.91619.1.sa0

N/A

0DataRank · unranked

0 citations

Edmond M. Linossi, Christian B. Macdonald, Carla A. Espinoza, Jennifer M. Michaud, Willow Coyote-Maestas +4 more

Reviewer #1 (Public Review): Conserved regulatory motifs in the juxtamembrane domain and kinase N-lobe revealed through deep mutational scanning of the MET receptor tyrosine kinase domain

(2023)10.7554/elife.91619.1.sa1

N/A

0DataRank · unranked

0 citations

Edmond M. Linossi, Christian B. Macdonald, Carla A. Espinoza, Jennifer M. Michaud, Willow Coyote‐Maestas +4 more

Structure is beauty, but not always truth

Cell(2024)10.1016/j.cell.2024.01.003

N/A

0DataRank · unranked

44 citations

Mark A. Murcko, James S. Fraser

Automated multiconformer model building for X-ray crystallography and cryo-EM

eLife(2024)10.7554/elife.90606.3

N/A

0DataRank · unranked

17 citations

Ashraya Ravikumar, Shivani Sharma, Blake T. Riley, Akshay Raju, Daniel W. Hogan +5 more

An ILC2-chitinase circuit restores lung homeostasis after epithelial injury

Science Immunology(2024)10.1126/sciimmunol.adl2986

N/A

0DataRank · unranked

12 citations

Do-Hyun Kim, Roberto Efraín Díaz, J. Michael White, Summer Rucknagel, Lauryn Mosby +10 more

Comprehensive encoding of conformational and compositional protein structural ensembles through the mmCIF data structure

IUCrJ(2024)10.1107/s2052252524005098

N/A

0DataRank · unranked

17 citations

James S. Fraser, Stephanie A. Wankowicz

The impact of Library Size and Scale of Testing on Virtual Screening

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.07.08.602536

N/A

0DataRank · unranked

7 citations

Olivier Mailhot, Isabella Glenn, Seth F. Vigneron, Violla Bassim, Xinyu Xu +8 more

Mapping kinase domain resistance mechanisms for the MET receptor tyrosine kinase via deep mutational scanning

eLife(2024)10.7554/elife.101882

N/A

0DataRank · unranked

12 citations

Edmond M. Linossi, J. N. K. Rao, Christian B. Macdonald, Ashraya Ravikumar, Karson M Chrispens +7 more

Comprehensive Encoding of Conformational and Compositional Protein Structural Ensembles through mmCIF Data Structure

ChemRxiv(2024)10.26434/chemrxiv-2023-ggd1w-v3

N/A

0DataRank · unranked

9 citations

James S. Fraser, Stephanie A. Wankowicz

Extensive exploration of structure activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment merging and active learning

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.08.25.609621

N/A

0DataRank · unranked

9 citations

Moira Rachman, Takaya Togo, Stefan Gahbauer, Yagmur U. Doruk, Maisie GV Stevens +12 more

Making sense of chaos: uncovering the mechanisms of conformational entropy

ChemRxiv(2024)10.26434/chemrxiv-2023-9b5k7-v3

N/A

0DataRank · unranked

6 citations

James S. Fraser, Stephanie A. Wankowicz

Making sense of chaos: uncovering the mechanisms of conformational entropy

ChemRxiv(2024)10.26434/chemrxiv-2023-9b5k7-v2

N/A

0DataRank · unranked

2 citations

James S. Fraser, Stephanie A. Wankowicz

Deep mutational scanning of EccD 3 reveals the molecular basis of its essentiality in the mycobacterium ESX secretion system

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.08.23.609456

N/A

0DataRank · unranked

2 citations

Christian B. Macdonald, Oren S. Rosenberg, James S. Fraser, Willow Coyote‐Maestas, Donovan Trinidad

Expanding Automated Multiconformer Ligand Modeling to Macrocycles and Fragments

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.09.20.613996

N/A

0DataRank · unranked

1 citations

Nathaniel Echols, G.J. Correy, Priya Jaishankar, Takaya Togo, Adam R. Renslo +4 more

Uncovering Protein Ensembles: Automated Multiconformer Model Building for X- ray Crystallography and Cryo-EM

eLife(2024)10.7554/elife.90606.2

N/A

0DataRank · unranked

0 citations

Ashraya Ravikumar, Shivani Sharma, Blake T. Riley, Akshay Raju, Jessica Flowers +5 more

Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase

eLife(2024)10.7554/elife.89918.2

N/A

0DataRank · unranked

0 citations

Andrew K. Ecker, G.J. Correy, Pooja Asthana, I.D. Young, Bryan Faust +6 more

AcrIF11 is a potent CRISPR-specific ADP-ribosyltransferase encoded by phage and plasmid

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.08.26.609590

N/A

0DataRank · unranked

0 citations

Leah T. Roe, Yuping Li, Adair L. Borges, Jenny Y. Zhang, Palak Babbar +11 more

Ribosomal RNA methylation by GidB modulates discrimination of mischarged tRNA

eLife(2024)10.7554/elife.102752

N/A

0DataRank · unranked

0 citations

Yuxiang Chen, I.D. Young, Hong-Wei Su, Yuemeng Chen, Jia-Yao Hong +3 more

Author response: Uncovering Protein Ensembles: Automated Multiconformer Model Building for X- ray Crystallography and Cryo-EM

(2024)10.7554/elife.90606.2.sa4

N/A

0DataRank · unranked

0 citations

Ashraya Ravikumar, Shivani Sharma, Blake T. Riley, Akshay Raju, Jessica Flowers +5 more

The impact of library size and scale of testing on virtual screening

Nature Chemical Biology(2025)10.1038/s41589-024-01797-w

N/A

0DataRank · unranked

42 citations

Olivier Mailhot, Isabella Glenn, Seth F. Vigneron, Violla Bassim, Xinyu Xu +8 more

Distal mutations enhance catalysis in designed enzymes by facilitating substrate binding and product release

Nature Communications(2025)10.1038/s41467-025-63802-7

N/A

0DataRank · unranked

19 citations

Pooja Asthana, Hiva Doustmohammadi, Cindy Klaus, Janet Sánchez, Serena E. Hunt +5 more

AcrIF11 is a potent CRISPR-specific ADP-ribosyltransferase encoded by phage and plasmid

mBio(2025)10.1128/mbio.01698-25

N/A

0DataRank · unranked

4 citations

Leah T. Roe, Yuping Li, Adair L. Borges, Jenny Y. Zhang, Palak Babbar +11 more

Hybrid Antibiotics Targeting the Bacterial Ribosome

ACS Central Science(2025)10.1021/acscentsci.5c01046

N/A

0DataRank · unranked

3 citations

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Bioinformatics Advances(2025)10.1093/bioadv/vbaf218

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0DataRank · unranked

1 citations

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MET variants with activating N‐lobe mutations identified in hereditary papillary renal cell carcinomas still require ligand stimulation

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N/A

0DataRank · unranked

3 citations

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eLife(2025)10.7554/elife.103797

N/A

0DataRank · unranked

10 citations

Nathaniel Echols, G.J. Correy, Priya Jaishankar, Takaya Togo, Adam R. Renslo +4 more

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eLife(2025)10.7554/elife.103484

N/A

0DataRank · unranked

7 citations

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bioRxiv (Cold Spring Harbor Laboratory)(2025)10.64898/2025.12.25.696505

N/A

0DataRank · unranked

5 citations

G.J. Correy, Brendan W. Hall, Moira Rachman, Olivier Mailhot, Takaya Togo +15 more

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bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.10.11.681833

N/A

0DataRank · unranked

3 citations

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Structure-based discovery of inhibitors of Mac1 domain of nonstructural protein-3 of SARS-CoV-2 by machine learning-augmented screening of chemical space

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.09.05.674529

N/A

0DataRank · unranked

2 citations

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Bayesian multi-state multi-condition modeling of a protein structure based on X-ray crystallography data

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.10.07.680994

N/A

0DataRank · unranked

1 citations

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bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.02.16.638509

N/A

0DataRank · unranked

0 citations

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Hybrid antibiotics targeting the bacterial ribosome

ChemRxiv(2025)10.26434/chemrxiv-2025-bxcn7

N/A

0DataRank · unranked

0 citations

J. Pellegrino, Tushar Raskar, Minh L. N. Tran, Mohamad Dandan, François Guérin +5 more

Expanding Automated Multiconformer Ligand Modeling to Macrocycles and Fragments

eLife(2025)10.7554/elife.103797.2

N/A

0DataRank · unranked

0 citations

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ChemRxiv(2025)10.26434/chemrxiv-2025-7n89p

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0DataRank · unranked

0 citations

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(2025)10.7554/elife.106484.2.sa0

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0DataRank · unranked

0 citations

Jyoti Batra, Monita Muralidharan, Shivali Malpotra, Durga Anand, Rachel Bauer +6 more

Coupled equilibria of dimerization and lipid binding modulate SARS Cov 2 Orf9b interactions and interferon response

eLife(2025)10.7554/elife.106484.2

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0DataRank · unranked

0 citations

Jyoti Batra, Monita Muralidharan, Shivali Malpotra, Durga Anand, Rachel Bauer +6 more

Initial leads to combat streptogramin resistance generated from X-ray fragment screening against VatD

Structure(2025)10.1016/j.str.2025.08.017

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0DataRank · unranked

0 citations

Sonya Lee, Christian M. MacDonald, Ian B. Seiple, James S. Fraser, Pooja Asthana

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ChemRxiv(2025)10.26434/chemrxiv-2025-d1v7v

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0DataRank · unranked

0 citations

Madhushika Silva, G.J. Correy, Abd Al‐Aziz A. Abu‐Saleh, Suzanne Ackloo, C. Arrowsmith +74 more

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bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.10.09.681498

N/A

0DataRank · unranked

0 citations

Lena Bergmann, Annabelle Henrion Lacritick, Jared C. Nigg, G.J. Correy, Alan Ashworth +3 more

Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico

Nature Communications(2020)10.1038/s41467-020-18619-x

N/A

0DataRank · unranked

128 citations

Rojo V. Rakotoharisoa, Michael C. Thompson, Niayesh Zarifi, Erin Nguyen, Nurzhan Mukhametzhanov +4 more

Synthetic group A streptogramin antibiotics that overcome Vat resistance

Nature(2020)10.1038/s41586-020-2761-3

N/A

0DataRank · unranked

118 citations

J. Pellegrino, D. John Lee, Arthur A. Tran, H.A. Chaires, Ruoxi Wang +17 more

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

Science(2020)10.1126/science.abc0881

N/A

0DataRank · unranked

81 citations

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

IUCrJ(2020)10.1107/s205225252000072x

N/A

0DataRank · unranked

50 citations

I.D. Young, Raymond G. Sierra, Aaron S. Brewster, Michael W. Martynowycz, Eriko Nango +33 more

Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit

Nucleic Acids Research(2020)10.1093/nar/gkaa037

N/A

0DataRank · unranked

29 citations

Alexander G. Myasnikov, I.D. Young, Adam Frost, James S. Fraser, Danica Galonić Fujimori +1 more

What Will Computational Modeling Approaches Have to Say in the Era of Atomistic Cryo-EM Data?

Journal of Chemical Information and Modeling(2020)10.1021/acs.jcim.0c00123

N/A

0DataRank · unranked

25 citations

Kresten Lindorff‐Larsen, Massimiliano Bonomi, James S. Fraser

Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.24.393405

N/A

0DataRank · unranked

41 citations

G.J. Correy, Stefan Gahbauer, D. Fearon, Taiasean Wu, Roberto Efraín Díaz +47 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.19.999235

N/A

0DataRank · unranked

16 citations

Rojo V. Rakotoharisoa, Michael C. Thompson, Niayesh Zarifi, Erin Nguyen, Nurzhan Mukhametzhanov +4 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.09.03.280222

N/A

0DataRank · unranked

10 citations

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