Publications by authors named "Jeffrey Gray"

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What does AlphaFold3 learn about antibody and nanobody docking, and what remains unsolved?
Fatima N Hitawala, Jeffrey J Gray

MAbs· December 2025

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Adapting Co-Folding Models for Structure-Based Protein-Protein Docking Through Flow Matching.
Da Xu, Lee-Shin Chu, Jeffrey J Gray

bioRxiv· December 2025

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Can We Extract Physics-like Energies from Generative Protein Diffusion Models?
Sudeep Sarma, Harrison Truscott, Da Xu, Kendall Reid, Lee-Shin Chu, Jeffrey J Gray

bioRxiv· December 2025

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Fitness Landscape for Antibodies 2: Benchmarking Reveals That Protein AI Models Cannot Yet Consistently Predict Developability Properties.
Michael Chungyoun, Jeffrey Gray

bioRxiv· December 2025

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Evaluation of De Novo Deep Learning Models on the Protein-Sugar Interactome.
Samuel W Canner, Lei Lu, Sho S Takeshita, Jeffrey J Gray

bioRxiv· September 2025

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Docking With Rosetta and Deep Learning Approaches in CAPRI Rounds 47-55.
Ameya Harmalkar, Lee-Shin Chu, Samuel W Canner, Rituparna Samanta, Rahel Frick, Jeffrey J Gray

Proteins· September 2025

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Discovery of a single-subunit oligosaccharyltransferase that enables glycosylation of full-length IgG antibodies in bacteria.
Belen Sotomayor, Thomas C Donahue, Sai Pooja Mahajan, May N Taw, Sophia W Hulbert, Jeffrey J Gray

Nat Commun· July 2025

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Reliable protein-protein docking with AlphaFold, Rosetta, and replica exchange.
Ameya Harmalkar, Sergey Lyskov, Jeffrey J Gray

Elife· May 2025

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How well do contextual protein encodings learn structure, function, and evolutionary context?
Sai Pooja Mahajan, Fátima A Dávila-Hernández, Jeffrey A Ruffolo, Jeffrey J Gray

Cell Syst· March 2025

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Predictions from Deep Learning Propose Substantial Protein-Carbohydrate Interplay.
Samuel W Canner, Ronald L Schnaar, Jeffrey J Gray

bioRxiv· March 2025

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Anti-citrullinated protein antibodies arise during affinity maturation of germline antibodies to carbamylated proteins in rheumatoid arthritis.
Marta Escarra-Senmarti, Michael Chungyoun, Dylan Ferris, Jeffrey J Gray, Felipe Andrade

bioRxiv· March 2025

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Molecular Display of the Animal Meta-Venome for Discovery of Novel Therapeutic Peptides.
Meng-Hsuan Hsiao, Yang Miao, Zixing Liu, Konstantin Schütze, Nathachit Limjunyawong, Jeffrey J Gray

Mol Cell Proteomics· February 2025

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What does AlphaFold3 learn about antigen and nanobody docking, and what remains unsolved?
Fatima N Hitawala, Jeffrey J Gray

bioRxiv· January 2025

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Career advancement insights from certified pharmacy technicians: Enhanced opportunities for the pharmacy technician workforce.
Jeffrey A Gray, Michelle E Rapier, Jessica M Robinson, James S Wheeler

J Am Pharm Assoc (2003)· December 2024

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Advancing Membrane-Associated Protein Docking with Improved Sampling and Scoring in Rosetta.
Rituparna Samanta, Ameya Harmalkar, Priyamvada Prathima, Jeffrey J Gray

J Chem Theory Comput· December 2024

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Discovery of a single-subunit oligosaccharyltransferase that enables glycosylation of full-length IgG antibodies in .
Belen Sotomayor, Thomas C Donahue, Sai Pooja Mahajan, May N Taw, Sophia W Hulbert, Jeffrey J Gray

bioRxiv· November 2024

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Unified Sampling and Ranking for Protein Docking with DFMDock.
Lee-Shin Chu, Sudeep Sarma, Jeffrey J Gray

bioRxiv· September 2024

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The Human Ganglioside Interactome in Live Cells Revealed Using Clickable Photoaffinity Ganglioside Probes.
Gao-Lan Zhang, Mitchell J Porter, Abduselam K Awol, Benjamin C Orsburn, Samuel W Canner, Jeffrey J Gray

J Am Chem Soc· July 2024

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Advancing membrane-associated protein docking with improved sampling and scoring in Rosetta.
Rituparna Samanta, Ameya Harmalkar, Priyamvada Prathima, Jeffrey J Gray

bioRxiv· July 2024

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Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.
Mark Hutchinson, Jeffrey A Ruffolo, Nantaporn Haskins, Michael Iannotti, Giuliana Vozza, Jeffrey J Gray

MAbs· June 2024

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Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design.
Jared Adolf-Bryfogle, Jason W Labonte, John C Kraft, Maxim Shapovalov, Sebastian Raemisch, Jeffrey J Gray

PLoS Comput Biol· June 2024

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Molecular Display of the Animal Meta-Venome for Discovery of Novel Therapeutic Peptides.
Meng-Hsuan Hsiao, Yang Miao, Zixing Liu, Konstantin Schütze, Nathachit Limjunyawong, Jeffrey J Gray

bioRxiv· May 2024

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Thermostability Enhancement of GH 62 α-l-Arabinofuranosidase by Directed Evolution and Rational Design.
Manoela Martins, Alberto M Dos Santos, Clauber H S da Costa, Samuel W Canner, Michael Chungyoun, Jeffrey J Gray

J Agric Food Chem· February 2024

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Efficacy of oral 20-hydroxyecdysone (BIO101), a MAS receptor activator, in adults with severe COVID-19 (COVA): a randomized, placebo-controlled, phase 2/3 trial.
Suzana Margareth Lobo, Gaétan Plantefève, Girish Nair, Adilson Joaquim Cavalcante, Nara Franzin de Moraes, Jeffrey Gray

EClinicalMedicine· February 2024

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Implicit model to capture electrostatic features of membrane environment.
Rituparna Samanta, Jeffrey J Gray

PLoS Comput Biol· January 2024

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