Jeffrey J. Gray

Also affiliated with Johns Hopkins Medicine

Biochemistry, Genetics and Molecular BiologyMedicineMaterials Science

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 1%percentile

4.8Author DataRank

Indexed papers

5in 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 5 indexed papers 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.

Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment

Proteins Structure Function and Bioinformatics(2021)10.1002/prot.26222

Top 9%

2.3DataRank

Top 9%127 citations

Guillaume Brysbaert, Théo Mauri, Nurul Nadzirin, Sameer Velankar, Raphaël A. G. Chaleil +95 more

Papers

Driven by 65 papers — median percentile 89. Top paper: “Toward high‐resolution homology modeling of antibody Fv regions and application to antibody–antigen docking”.

Toward high‐resolution homology modeling of antibody Fv regions and application to antibody–antigen docking

Proteins: Structure, Function, and Bioinformatics(2009)10.1002/prot.22309

N/A

8.1DataRank · unranked

188 citations

Aroop Sircar, Sidhartha Chaudhury, Jeffrey J. Gray, Arvind Sivasubramanian

Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment

Proteins Structure Function and Bioinformatics(2021)10.1002/prot.26222

Top 9%

2.3DataRank

Top 9%127 citations

Guillaume Brysbaert, Théo Mauri, Nurul Nadzirin, Sameer Velankar, Raphaël A. G. Chaleil +95 more

Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification

Frontiers in Immunology(2018)10.3389/fimmu.2018.00413

N/A

2.1DataRank · unranked

66 citations

Adnan Sljoka, Daisuke Kuroda, Nobuyuki Tsuchimura, Naoki Katoh, Kouhei Tsumoto +2 more

Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment

Proteins Structure Function and Bioinformatics(2023)10.1002/prot.26609

Top 11%

1.9DataRank

Top 11%81 citations

Guillaume Brysbaert, Nessim Raouraoua, Paul A. Bates, Marco Giulini, Rodrigo V. Honorato +95 more

Geometric potentials from deep learning improve prediction of CDR H3 loop structures

Bioinformatics(2020)10.1093/bioinformatics/btaa457

N/A

0.665DataRank · unranked

83 citations

Carlos Guerra, Sai Pooja Mahajan, Jeremias Sulam, Jeffrey J. Gray, Jeffrey A. Ruffolo

Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment

Utrecht University Repository (Utrecht University)(2023)10.22541/au.168888815.53957253/v1

Top 36%

0.540DataRank

Top 36%17 citations

Guillaume Brysbaert, Nessim Raouraoua, Paul A. Bates, Marco Giulini, Rodrigo V. Honorato +95 more

Discovery of a single-subunit oligosaccharyltransferase that enables glycosylation of full-length IgG antibodies in bacteria

Nature Communications(2025)10.1038/s41467-025-61440-7

N/A

0.292DataRank · unranked

6 citations

Thomas C. Donahue, Sai Pooja Mahajan, May N. Taw, Sophia W. Hulbert, Erik J. Bidstrup +11 more

PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design

Preprints.org(2020)10.20944/preprints202002.0097.v1

N/A

0DataRank · unranked

4 citations

Jared Adolf‐Bryfogle, Jason C. Klima, Sergey Lyskov, Jason W. Labonte, Steven J. Bertolani +16 more

Robustification of RosettaAntibody and Rosetta SnugDock

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.26.116210

N/A

0DataRank · unranked

3 citations

Rahel Frick, Jing Zhou, Jeffrey J. Gray, Jeliazko R. Jeliazkov

Structural basis for peptide substrate specificities of glycosyltransferase GalNAc-T2

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.25.171371

N/A

0DataRank · unranked

1 citations

Yashes Srinivasan, Jason W. Labonte, Matthew P. DeLisa, Jeffrey J. Gray, Sai Pooja Mahajan

Diverse scientific benchmarks for implicit membrane energy functions

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.23.168021

N/A

0DataRank · unranked

1 citations

Jeffrey J. Gray, Rebecca F. Alford

Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement

UNC Libraries(2020)10.17615/a2jg-d649

N/A

0DataRank · unranked

0 citations

Jane S. Richardson, Ian Davis, Ron Jacak, Andrew Leaver-Fay, Roland A. Pache +12 more

Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)

UNC Libraries(2020)10.17615/7c93-y342

N/A

0DataRank · unranked

0 citations

Tanja Kortemme, Benjamin Borgo, James J. Havranek, Fang‐Chieh Chou, Bryan S. Der +12 more

A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design

UNC Libraries(2020)10.17615/e400-1y21

N/A

0DataRank · unranked

0 citations

Lynda Gonzales, Rebecca F. Alford, Erin L. Dolan, Jeffrey J. Gray, Andrew Leaver-Fay

Alternative Computational Protocols for Supercharging Protein Surfaces for Reversible Unfolding and Retention of Stability

UNC Libraries(2020)10.17615/d0j8-zf32

N/A

0DataRank · unranked

0 citations

George Georgiou, Ron Jacak, Jeffrey J. Gray, Brian Kuhlman, Sergey Lyskov +4 more

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

UNC Libraries(2020)10.17615/6sk2-v510

N/A

0DataRank · unranked

0 citations

Matthew J. O’Meara, Philip Bradley, Maxim V. Shapovalov, Rhiju Das, Hahnbeom Park +15 more

Adding Diverse Noncanonical Backbones to Rosetta: Enabling Peptidomimetic Design

UNC Libraries(2020)10.17615/xrww-m716

N/A

0DataRank · unranked

0 citations

Brooke N. Bullock, Richard Bonneau, Paramjit S. Arora, Kent Kirshenbaum, Timothy W. Craven +14 more

Antibody structure prediction using interpretable deep learning

Patterns(2021)10.1016/j.patter.2021.100406

N/A

0DataRank · unranked

214 citations

Jeremias Sulam, Jeffrey J. Gray, Jeffrey A. Ruffolo

An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants

Structure(2021)10.1016/j.str.2021.01.005

N/A

0DataRank · unranked

125 citations

Thom Vreven, Jing Zhou, Iain H. Moal, Jeliazko R. Jeliazkov, Jeffrey J. Gray +3 more

Robustification of RosettaAntibody and Rosetta SnugDock

PLoS ONE(2021)10.1371/journal.pone.0234282

N/A

0DataRank · unranked

40 citations

Rahel Frick, Jing Zhou, Jeffrey J. Gray, Jeliazko R. Jeliazkov

A high-affinity human TCR-like antibody detects celiac disease gluten peptide–MHC complexes and inhibits T cell activation

Science Immunology(2021)10.1126/sciimmunol.abg4925

N/A

0DataRank · unranked

34 citations

Lene S. Høydahl, Jan Petersen, M. Fleur du Pré, Shraddha Kumari, Grete Berntsen +15 more

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

Nature Communications(2021)10.1038/s41467-021-27222-7

N/A

0DataRank · unranked

27 citations

Sergey Lyskov, Steven M. Lewis, Jared Adolf‐Bryfogle, Rebecca F. Alford, Kyle A. Barlow +45 more

Shotgun scanning glycomutagenesis: A simple and efficient strategy for constructing and characterizing neoglycoproteins

Proceedings of the National Academy of Sciences(2021)10.1073/pnas.2107440118

N/A

0DataRank · unranked

20 citations

Xiaolu Zheng, Sudhanshu Shanker, Thapakorn Jaroentomeechai, Tyler D. Moeller, Sophia W. Hulbert +9 more

Generative language modeling for antibody design

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.12.13.472419

N/A

0DataRank · unranked

48 citations

Jeffrey A. Ruffolo, Jeffrey J. Gray, Richard W. Shuai

Antibody structure prediction using interpretable deep learning

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.05.27.445982

N/A

0DataRank · unranked

22 citations

Jeremias Sulam, Jeffrey J. Gray, Jeffrey A. Ruffolo

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

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.04.438423

N/A

0DataRank · unranked

4 citations

Sergey Lyskov, Steven M. Lewis, Jared Adolf‐Bryfogle, Rebecca F. Alford, Kyle A. Barlow +43 more

Improved antibody structure prediction by deep learning of side chain conformations

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.22.461349

N/A

0DataRank · unranked

4 citations

Jeffrey A. Ruffolo, Sai Pooja Mahajan, Jeffrey J. Gray, Deniz Akpinaroglu

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

Hallucinating structure-conditioned antibody libraries for target-specific binders

Frontiers in Immunology(2022)10.3389/fimmu.2022.999034

N/A

0DataRank · unranked

21 citations

Jeffrey A. Ruffolo, Rahel Frick, Jeffrey J. Gray, Sai Pooja Mahajan

Induced fit with replica exchange improves protein complex structure prediction

PLoS Computational Biology(2022)10.1371/journal.pcbi.1010124

N/A

0DataRank · unranked

16 citations

Sai Pooja Mahajan, Jeffrey J. Gray, Ameya Harmalkar

Simultaneous prediction of antibody backbone and side-chain conformations with deep learning

PLoS ONE(2022)10.1371/journal.pone.0258173

N/A

0DataRank · unranked

16 citations

Jeffrey A. Ruffolo, Sai Pooja Mahajan, Jeffrey J. Gray, Deniz Akpinaroglu

De novo design and Rosetta‐based assessment of high‐affinity antibody variable regions (Fv) against the SARS‐CoV ‐2 spike receptor binding domain ( RBD )

Proteins Structure Function and Bioinformatics(2022)10.1002/prot.26422

N/A

0DataRank · unranked

16 citations

Ratul Chowdhury, Ranjani Ramasubramanian, Brandon Ameglio, Rahel Frick, Jeffrey J. Gray +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

Affinity maturation of TCR-like antibodies using phage display guided by structural modeling

Protein Engineering Design and Selection(2022)10.1093/protein/gzac005

N/A

0DataRank · unranked

2 citations

Lene S. Høydahl, Ina Hodnebrug, Erik Sebastian Vik, Bjørn Dalhus, Ludvig M. Sollid +4 more

Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.20.488972

N/A

0DataRank · unranked

35 citations

Lee‐Shin Chu, Sai Pooja Mahajan, Jeffrey J. Gray, Jeffrey A. Ruffolo

Hallucinating structure-conditioned antibody libraries for target-specific binders

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.06.06.494991

N/A

0DataRank · unranked

1 citations

Jeffrey A. Ruffolo, Rahel Frick, Jeffrey J. Gray, Sai Pooja Mahajan

Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies

Nature Communications(2023)10.1038/s41467-023-38063-x

N/A

0DataRank · unranked

317 citations

Lee‐Shin Chu, Sai Pooja Mahajan, Jeffrey J. Gray, Jeffrey A. Ruffolo

IgLM: Infilling language modeling for antibody sequence design

Cell Systems(2023)10.1016/j.cels.2023.10.001

N/A

0DataRank · unranked

128 citations

Jeffrey A. Ruffolo, Jeffrey J. Gray, Richard W. Shuai

Toward generalizable prediction of antibody thermostability using machine learning on sequence and structure features

mAbs(2023)10.1080/19420862.2022.2163584

N/A

0DataRank · unranked

50 citations

Roshan Rao, Yuxuan Richard Xie, Jonas Honer, Wibke Deisting, Jonas Anlahr +12 more

AI models for protein design are driving antibody engineering

Current Opinion in Biomedical Engineering(2023)10.1016/j.cobme.2023.100473

N/A

0DataRank · unranked

39 citations

Jeffrey J. Gray, Michael Chungyoun

Flexible protein–protein docking with a multitrack iterative transformer

Protein Science(2023)10.1002/pro.4862

N/A

0DataRank · unranked

32 citations

Jeffrey A. Ruffolo, Ameya Harmalkar, Jeffrey J. Gray, Lee‐Shin Chu

Structure-based neural network protein–carbohydrate interaction predictions at the residue level

Frontiers in Bioinformatics(2023)10.3389/fbinf.2023.1186531

N/A

0DataRank · unranked

22 citations

Sudhanshu Shanker, Jeffrey J. Gray, Samuel W. Canner

Fate and Efficacy of Engineered Allogeneic Stem Cells Targeting Cell Death and Proliferation Pathways in Primary and Brain Metastatic Lung Cancer

Stem Cells Translational Medicine(2023)10.1093/stcltm/szad033

N/A

0DataRank · unranked

3 citations

Yohei Kitamura, Paulo Borges, Sophia Auduong, Seyda Kilic, David Y.B. Deng +8 more

Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.29.547134

N/A

0DataRank · unranked

7 citations

Jeffrey A. Ruffolo, Ameya Harmalkar, Jeffrey J. Gray, Lee‐Shin Chu

Contextual protein and antibody encodings from equivariant graph transformers

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.15.549154

N/A

0DataRank · unranked

4 citations

Jeffrey A. Ruffolo, Jeffrey J. Gray, Sai Pooja Mahajan

Structure-Based Neural Network Protein-Carbohydrate Interaction Predictions at the Residue Level

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.14.531382

N/A

0DataRank · unranked

0 citations

Sudhanshu Shanker, Jeffrey J. Gray, Samuel W. Canner

The Human Ganglioside Interactome in Live Cells Revealed Using Clickable Photoaffinity Ganglioside Probes

Journal of the American Chemical Society(2024)10.1021/jacs.4c03196

N/A

0DataRank · unranked

24 citations

Mitchell J. Porter, Abduselam K. Awol, Benjamin C. Orsburn, Samuel W. Canner, Jeffrey J. Gray +4 more

Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen

mAbs(2024)10.1080/19420862.2024.2362775

N/A

0DataRank · unranked

17 citations

Jeffrey A. Ruffolo, Nantaporn Haskins, Michael J. Iannotti, Giuliana Vozza, Tony Pham +10 more

Molecular Display of the Animal Meta-Venome for Discovery of Novel Therapeutic Peptides

Molecular & Cellular Proteomics(2024)10.1016/j.mcpro.2024.100901

N/A

0DataRank · unranked

3 citations

Yang Miao, Zixing Liu, Konstantin Schütze, Nathachit Limjunyawong, Daphne Chun-Che Chien +11 more

Reliable protein–protein docking with AlphaFold, Rosetta, and replica exchange

eLife(2024)10.7554/elife.94029

N/A

0DataRank · unranked

6 citations

Sergey Lyskov, Jeffrey J. Gray, Ameya Harmalkar

Unified Sampling and Ranking for Protein Docking with DFMDock

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.09.27.615401

N/A

0DataRank · unranked

5 citations

Sudeep Sarma, Da Xu, Jeffrey J. Gray, Lee‐Shin Chu

Discovery of a single-subunit oligosaccharyltransferase that enables glycosylation of full-length IgG antibodies in Escherichia coli

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.08.12.607630

N/A

0DataRank · unranked

1 citations

Thomas C. Donahue, Sai Pooja Mahajan, May N. Taw, Sophia W. Hulbert, Erik J. Bidstrup +11 more

Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules

UNC Libraries(2020)10.17615/8ga2-9t05

N/A

0DataRank · unranked

149 citations

Monica Berrondo, Andrew Leaver-Fay, James Thompson, S. I. Cooper, Daniel J. Mandell +27 more

Reliable protein–protein docking with AlphaFold, Rosetta, and replica exchange

eLife(2025)10.7554/elife.94029.3

N/A

0DataRank · unranked

15 citations

Sergey Lyskov, Jeffrey J. Gray, Ameya Harmalkar

Evaluation of De Novo Deep Learning Models on the Protein-Sugar Interactome

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.09.02.673778

N/A

0DataRank · unranked

2 citations

Lei Lü, Sho S Takeshita, Jeffrey J. Gray, Samuel W. Canner

How well do contextual protein encodings learn structure, function, and evolutionary context?

Cell Systems(2025)10.1016/j.cels.2025.101201

N/A

0DataRank · unranked

0 citations

Fátima A. Dávila-Hernández, Jeffrey A. Ruffolo, Jeffrey J. Gray, Sai Pooja Mahajan

Unified Sampling and Ranking for Protein Docking with DFMDock

(2025)10.22541/au.175356366.67982417/v1

N/A

0DataRank · unranked

0 citations

Sudeep Sarma, Da Xu, Jeffrey J. Gray, Lee‐Shin Chu

Docking With Rosetta and Deep Learning Approaches in CAPRI Rounds 47–55

Proteins Structure Function and Bioinformatics(2025)10.1002/prot.70016

N/A

0DataRank · unranked

0 citations

Lee‐Shin Chu, Samuel W. Canner, Rituparna Samanta, Rahel Frick, Fátima A. Dávila-Hernández +4 more

Molecular Display of the Animal Meta-Venome for Discovery of Novel Therapeutic Peptides

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.05.27.595990

N/A

0DataRank · unranked

0 citations

Yang Miao, Zixing Liu, Konstantin Schütze, Nathachit Limjunyawong, Daphne Chun-Che Chien +11 more

Deep Learning in Protein Structural Modeling and Design

Patterns(2020)10.1016/j.patter.2020.100142

N/A

0DataRank · unranked

227 citations

Sai Pooja Mahajan, Jeremias Sulam, Jeffrey J. Gray, Wenhao Gao

Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane

Biophysical Journal(2020)10.1016/j.bpj.2020.03.006

N/A

0DataRank · unranked

88 citations

Patrick J. Fleming, Karen G. Fleming, Jeffrey J. Gray, Rebecca F. Alford

Advances to tackle backbone flexibility in protein docking

Current Opinion in Structural Biology(2020)10.1016/j.sbi.2020.11.011

N/A

0DataRank · unranked

65 citations

Jeffrey J. Gray, Ameya Harmalkar

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

PLoS Computational Biology(2020)10.1371/journal.pcbi.1007507

N/A

0DataRank · unranked

44 citations

Brian D. Weitzner, P. Douglas Renfrew, Steven M. Lewis, Rocco Moretti, Andrew M. Watkins +20 more

Geometric Potentials from Deep Learning Improve Prediction of CDR H3 Loop Structures

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.02.09.940254

N/A

0DataRank · unranked

8 citations

Carlos Guerra, Sai Pooja Mahajan, Jeremias Sulam, Jeffrey J. Gray, Jeffrey A. Ruffolo

Shotgun scanning glycomutagenesis: a simple and efficient strategy for constructing and characterizing neoglycoproteins

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.28.176198

N/A

0DataRank · unranked

6 citations

Xiaolu Zheng, Sudhanshu Shanker, Thapakorn Jaroentomeechai, Tyler D. Moeller, Sophia W. Hulbert +9 more

Jeffrey J. Gray

Indexed papers

Top data-sharing exemplar

Papers