# Prediction of the Structures of Protein Complexes

> **NIH NIH R35** · JOHNS HOPKINS UNIVERSITY · 2022 · $791,648

## Abstract

Prediction of the Structures of Protein Complexes
Jeffrey J. Gray, NIGMS R35 (MIRA)
PROJECT SUMMARY
Protein interactions are involved in nearly all biological processes in human health and diseases, and protein
complex structures can reveal biological mechanisms and suggest intervention strategies. Computational
modeling provides an alternative route to elucidate structures. Modeling also tests our understanding of
molecular biophysics and allows us to engineer molecules based on their structures. My lab is a pioneer in
developing computational methods to predict and design protein–protein interfaces and in applying those
methods broadly, from immunology and cancer to infectious disease and tissue engineering. Our central focus
is on protein–protein docking, that is, predicting the structure of a complex from the components (individual
polypeptides or domains). A longstanding challenge in docking is correctly capturing protein conformational
change, and we lead development of innovative search strategies and rapid scoring schemes to close this gap.
Another focus area is the modeling and design of antibodies, directly supporting drug and diagnostic agent
development and optimization. We predict high-resolution antibody structures from sequence, dock those
models to antigens, and design antibodies to target specific antigens. Several protein modifications are important
to consider when modeling interfaces. The emergence of powerful experimental methods for characterizing
glycans has prompted us to expand our tools to model carbohydrates including docking methods and focused
studies on glycotransferases. All our methods are embedded in the Rosetta software platform, which is used by
tens of thousands of academic and industry scientists worldwide. The utility of our work is evidenced by the high
demand for our prediction and design web server, scripting platform, and teaching materials. By leading the
technical and scientific testing operations for the Rosetta Commons, my lab powers the synergies to combine
Rosetta's powerful biomolecular prediction and design methods across this international collaboration.

## Key facts

- **NIH application ID:** 10407529
- **Project number:** 5R35GM141881-02
- **Recipient organization:** JOHNS HOPKINS UNIVERSITY
- **Principal Investigator:** JEFFREY J GRAY
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $791,648
- **Award type:** 5
- **Project period:** 2021-06-01 → 2026-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10407529

## Citation

> US National Institutes of Health, RePORTER application 10407529, Prediction of the Structures of Protein Complexes (5R35GM141881-02). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10407529. Licensed CC0.

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