Research Areas Protein structure prediction and design Protein-protein docking Antibody engineering Deep learning Membrane protein modeling Glycoprotein modeling

Jeffrey Gray, a Johns Hopkins University Provost’s Discovery Award recipient, is the creator of a pioneering computer code architecture used by thousands of biomedical researchers worldwide to predict and design protein structure. The computational tools he and his lab, GrayLab, develop are furthering capabilities to resolve disease and immunity, including cell signaling, DNA regulation, Alzheimer’s disease, HIV, and cancer. He is a professor of chemical and biomolecular engineering.

Gray is the original developer of RosettaDock, a multi-scale algorithm and leading tool for the prediction of the structure of protein complexes from their constituent proteins. Protein docking is critical for deciphering molecular mechanisms. Gray’s team pioneered key methods in exploring diverse conformations, evaluating candidate structures, and deploying advanced optimization algorithms on supercomputing facilities to enable consistent and accurate results.

GrayLab also developed extensive tools for antibody engineering. Central to adaptive immune system function, antibodies comprise one-third of the pharmaceuticals in development and are critical biotechnological molecules for reagents, tags, and sensors. His team has predicted antibody structures and antibody-antigen complex structures identified the origin of specificity and mechanisms of antibody evolution and created tools for the design of robust biologics for use as pharmaceuticals.

His lab also created the first structure prediction and design algorithms for proteins interacting with solid surfaces, which is vital in bionanotechnology and in biomineralization processes such as the creation of bone and teeth. In addition, the GrayLab developed the first computational designs of peptides that bind calcite and affect mineral growth, toward an ultimate goal of using designed proteins to control material synthesis on the molecular scale. New research projects focus on protein-glycan interactions, membrane protein structure, and protein crystal design.

As one of 50 international Rosetta Commons labs, Gray’s GrayLab shares biomolecular modeling and design code in real-time and distributes it free of charge to academics and nonprofits. Gray’s antibody and docking algorithms are highly sought by academic and industry researchers; the ROSIE web server includes these apps and has performed more than 64,000 jobs for the scientific community.  The Rosetta code has been licensed to over 32,000 academics and 84 companies (including startups and industry leaders such as GlaxoSmithKline, Pfizer, Merck).  Gray’s team leads the technical and scientific code testing for the Commons. Gray serves as the Rosetta Commons Diversity Chair, is a member of its Executive Committee, and directs the National Science Foundation (NSF)-supported Rosetta Commons Summer Intern Program.

Gray, who is affiliated with Hopkins’ Program in Molecular Biophysics, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, and Institute for NanoBioTechnology, has garnered numerous awards for his research. Selected honors include a National Institutes of Health (NIH) K01 Mentored Quantitative Research Fellowship in Genomics, NSF Career Award, and a Beckman Young Investigator Award. In 2016, Gray was named to the College of Fellows, American Institute for Medical and Biological Engineering, and won the David Himmelblau Award for Innovations in Computer-Based Chemical Engineering Education. At Johns Hopkins, he has been recognized with the F. Stuart Hodgson Faculty Scholar, the Provost’s Discovery Award, and the Alumni Association Excellence in Teaching Award honors.

 A sought-after lecturer, Gray most recently presented the Inaugural Professorial Lecture, Whiting School of Engineering, JHU (2015), the Computational Molecular Science & Engineering Forum (ComSEF) Plenary Lecture at the 2015 Association of International Chemical Engineers (AIChE) National Meeting, and the Centennial Lecturer, McKetta Department of Chemical Engineering at the University of Texas at Austin, also in 2015. In addition to his service on Rosetta’s advisory board, Gray is an ad hoc reviewer for NIH and serves on the editorial board of Proteins: Structure, Function, and Bioinformatics. A passionate advocate for STEM education and diversity, he was a board member of Baltimore’s Ingenuity Project from 2005 to 2016, served on the Faculty Outreach Oversight Board, STEM Achievement in Baltimore Schools, co-chaired the Faculty Recruitment and Development Subcommittee of the JHU Diversity Leadership Council, and founded and chaired Johns Hopkins’ Homewood Council on Inclusive Excellence[SA2].

He received his BSE in Chemical Engineering at the University of Michigan and his PhD in Chemical Engineering at the University of Texas at Austin, completing post-doctoral training researching protein-protein docking at the University of Washington.