Award Abstract # 1950697
REU Site: A Cyberlinked Program in Computational Biomolecular Structure & Design

NSF Org: DBI
Division of Biological Infrastructure
Recipient: THE JOHNS HOPKINS UNIVERSITY
Initial Amendment Date: February 25, 2020
Latest Amendment Date: July 30, 2021
Award Number: 1950697
Award Instrument: Continuing Grant
Program Manager: Andrea Holgado de Brigueda
DBI
 Division of Biological Infrastructure
BIO
 Directorate for Biological Sciences
Start Date: March 1, 2020
End Date: August 31, 2023 (Estimated)
Total Intended Award Amount: $485,383.00
Total Awarded Amount to Date: $535,443.00
Funds Obligated to Date: FY 2020 = $161,500.00
FY 2021 = $373,943.00
History of Investigator:
  • Jeffrey Gray (Principal Investigator)
    jgray@jhu.edu
Recipient Sponsored Research Office: Johns Hopkins University
3400 N CHARLES ST
BALTIMORE
MD  US  21218-2608
(443)997-1898
Sponsor Congressional District: 07
Primary Place of Performance: Johns Hopkins University
3400 N. Charles St.
Baltimore
MD  US  21218-2687
Primary Place of Performance
Congressional District:
07
Unique Entity Identifier (UEI): FTMTDMBR29C7
Parent UEI: GS4PNKTRNKL3
NSF Program(s): RSCH EXPER FOR UNDERGRAD SITES
Primary Program Source: 01002021DB NSF RESEARCH & RELATED ACTIVIT
01002122DB NSF RESEARCH & RELATED ACTIVIT

01002223DB NSF RESEARCH & RELATED ACTIVIT
Program Reference Code(s): 108Z, 102Z, 9250
Program Element Code(s): 113900
Award Agency Code: 4900
Fund Agency Code: 4900
Assistance Listing Number(s): 47.074

ABSTRACT

This REU Site award to Johns Hopkins University, located in Baltimore, MD, will support the training of 12 students for 10 weeks during the summers of 2020 - 2022. Research is conducted in various labs of the Rosetta Commons (http://www.rosettacommons.org) located throughout the United States and abroad. It is anticipated that a total of 36 students, primarily from schools with limited research opportunities or are from an under-represented group, 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 gain an understanding of how to investigate biological problems from a structural perspective; experience computational molecular design; acquire a solid foundation in research methodologies in biochemistry, biophysics, computational biology, and molecular engineering; gain skills to collaborate with other scientists and engineers in other laboratories globally; and gain a deeper appreciation for the contributions that improved technology in these areas can make to society. Assessment of the program will be done thru the SALG URSSA tool. Students will be tracked after the program in order to determine their career paths.

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?, ?Design of protein-based small molecule sensor/actuators?, and ?Modeling and designing RNA at high resolution?. The training program consists of a 1-week bootcamp where students learn computer coding and structural biology, 8 weeks of research in distributed labs (across the US and abroad), and a final week together at the annual Rosetta Conference. 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. More information about the program is available at http://www.rosettacommons.org/intern, or by contacting the PI (Dr. Jeffrey J. Gray at jgray@jhu.edu) or the program administrator (Ms. Camille Mathis at cmathis@jhu.edu).

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.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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Mahajan, Sai Pooja and Srinivasan, Yashes and Labonte, Jason W. and DeLisa, Matthew P. and Gray, Jeffrey J. "Structural Basis for Peptide Substrate Specificities of Glycosyltransferase GalNAc-T2" ACS Catalysis , v.11 , 2021 https://doi.org/10.1021/acscatal.0c04609 Citation Details
Biehn, Sarah E. and Picarello, Danielle M. and Pan, Xiao and Vachet, Richard W. and Lindert, Steffen "Accounting for Neighboring Residue Hydrophobicity in Diethylpyrocarbonate Labeling Mass Spectrometry Improves Rosetta Protein Structure Prediction" Journal of the American Society for Mass Spectrometry , v.33 , 2022 https://doi.org/10.1021/jasms.1c00373 Citation Details

PROJECT OUTCOMES REPORT

Disclaimer

This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.

The Rosetta Commons REU program provided summer research training for 61 students from summer 2021 through spring 2023 [summer cohorts for 2020, 2021, 2022, with some additional research continued remotely during the following school year.]. Seven of these students researched with and were funded by industry partners. The program collected 1,060 applications for admission during the three-year period. Of these 61 students, 18% identify as African American or Black, 7% identify as Latin or Hispanic, and 3% identify as multiracial. Sixty percent of the interns identify as female and 6% identify as non-binary or none.

This REU program has achieved its overall goal of engaging students through hands-on research experiences, following best practices for retaining students from diverse backgrounds, and providing unique experiences in cyber-enabled collaborative research. The program has also laid the foundation for interest in graduate research, future inters presentations, and published papers. After the REU, interns completed the SALG URSSA survey. Eighty-seven percent of interns reported that they are more likely to pursue a PhD in STEM because of the REU program. Ninety-eight percent of interns reported that the REU program prepared them for graduate school. All the interns surveyed rated the research experience as good to excellent.

The REU interns were trained on the Rosetta Commons software through a weeklong boot camp hosted at University of North Carolina, Chapel Hill. Training topics included Python instructions 1 and 2, C++ libraries, ligand docking, protein docking, and loop modeling, and much more. The interns were trained by faculty and former Rosetta Commons REU interns. The REU interns performed research in labs at various universities, including the University of Washington, Vanderbilt University, Harvard University, and the University of California, San Francisco.

The interns participated in responsible conduct of research training and were included in an REU program local to their host university, to provide them with a peer group and activities. The REU cohort used Zoom to meet for a virtual journal club, where each week, two interns lead a literature review and then made brief presentations on their research. Faculty mentors were present at each meeting to ask pointed questions and present a mini lesson. These faculty mentors covered topics including imposter syndrome, responding to critiques, and applying to graduate school. The interns were fully immersed in lab research and projects with intellectual merit.  Examples of projects during the summer of 2022 include:

  • Predictive models for binding and developability of antibodies
  • Antibody engineering by deep learning
  • Protein design for immunological intervention
  • Designing stimulus-responsive enzymes for targeted chemotherapy
  • Applying machine learning to protein design
  • Reshaping protein energy landscapes to optimize dynamics/function

This program engaged undergraduates in a cyberlinked REU program within a geographically distributed collaborative scientific community. It featured creative combinations of disciplines including biology, chemistry, computer science, and engineering. REU interns were vital in the planning and progress in their assigned projects. The projects promoted learning, skill development, career exploration, and teaching. At the end of the summer, the interns presented posters on their work at the annual RosettaCon conference. The conference also provided them an opportunity to network with faculty, industry researchers, and graduate students. Interns also attend talks by various researchers within the Rosetta Commons community.

Alumni from these three cohorts have gone on to pursue doctoral degrees at institutions including Stanford, Harvard, MIT, Pepperdine, University of Cambridge, and University of California, San Francisco. Other interns went into industry at Salesforce, Abbott, DE Shaw, Neural STEM Institute, and Hewlitt Packard. Money saved through efficient program budgeting was directed towards extending some intern’s research projects into the school year. These interns continued to work with their REU faculty mentor, remotely and increased their research progress and experience. Overall, the Rosetta Commons REU program has attracted, trained, and mentored a diverse group of interns.

 


Last Modified: 01/02/2024
Modified by: Jeffrey J Gray

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