Artificial Intelligence for Biomolecular Structure Prediction and Design

This REU Site award to Johns Hopkins University, located in Baltimore, MD, will support the training of 12 interns for 10 weeks during each summer from 2026 to 2028. Research is conducted in various labs of the Rosetta Commons located throughout the United States and abroad. It is anticipated that a total of 36 students, primarily from schools with limited research opportunities, will be trained in the program. Students will learn how interdisciplinary, collaborative research is conducted, and all will present their work at scientific conferences. Upon completion of the REU program, students will have gained an understanding of how to investigate biological problems from a structural perspective; experienced computational molecular design including artificial intelligence approaches; acquired a solid foundation in research methodologies in biochemistry, biophysics, computational biology, machine learning, and molecular engineering; gained skills to collaborate with other scientists and engineers in other laboratories globally; and gained a deeper appreciation for the contributions that improved technology in these areas can make to society. The program will be assessed using the SALG URSSA questionnaire through Qualtrics. The NSF ETAP system will be used to register participants (https://www.nsfetap.gov/). Students will be tracked after the program to determine their career paths. The training students will receive is aligned with the NSF priorities in Biotechnology, Quantum Information Science and Artificial Intelligence. The research uses computational methods for prediction of the structure of biomolecules (which underlies their behavior and function) and the design of new biomolecules (important for materials, nanotechnology, and biotechnology). Example research projects include “Antibody engineering by deep learning,” “Protein design using generative methods,” “Enzyme design through quantum active site modeling and diffusive scaffold generation,” and “Cracking the human immune repertoire using AI.” The training program consists of a one-week bootcamp where students learn computer coding and structural biology, eight weeks of research in distributed labs (across the US and abroad), and a final week together at the annual Rosetta Conference. One training module includes quantum mechanical approaches for active site design, and one mentor’s research focuses on enzyme design, which can begin from quantum calculations of transition states. During the research period, students will complete an independent research project under the mentorship of a host lab, participate in weekly virtual journal clubs, prepare research proposals, and prepare a poster for presentation at the conference. All participants complete the Responsible Conduct of Research course. REU applications are reviewed and chosen by an admissions committee consisting of Rosetta Commons members at all career levels. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria. NSF Award ID: 2548392 | Program: 01002627DB NSF RESEARCH & RELATED ACTIVIT | Principal Investigator: Jeffrey Gray | Institution: Johns Hopkins University, BALTIMORE, MD | Award Amount: $584,498 View on NSF Award Search: https://www.nsf.gov/awardsearch/show-award/?AWD_ID=2548392 View on Research.gov: https://www.research.gov/awardapi-service/v1/awards/2548392.html