Computational Biomolecular Structure & Design

Rosetta Commons Research Experience for Undergraduates

A Cyberlinked Program in Computational Biomolecular Structure & Design

Interns in this geographically-distributed REU program have the opportunity to participate in research using the Rosetta Commons software. The Rosetta Commons software suite includes algorithms for computational modeling and analysis of protein structures. It has enabled notable scientific advances in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.

We expect most internships will be in-person, but some institutions or applicants may require a virtual format.
We will adjust the program to conditions as needed.

The program:

One week of Rosetta Code School (June 5 through June 9) where you will learn the inner details of the RosettaPython code and community coding environment, so you are fully prepared for the summer!

8 weeks of hands-on research in a molecular modeling and design laboratory, developing new algorithms and discovering new science.

The summer will finish with a trip to the Rosetta Conference in the gorgeous Cascade Mountains of Washington State, where you will present your research in a poster and connect with Rosetta developers from around the world. The conference will be held from August 7 through August 10.

This program is supported by NSF (Award 1950697). Interns will receive housing, paid travel expenses, and a $6,000 stipend.

Program dates are June 5, 2023 - August 11, 2023.

To apply:

Include the following in the application:

• Resume
• Transcript
• Personal statement - why this internship interests you - brief summary of research and computing experience - why you are an appropriate candidate for the internship (up to 500 words, not characters)
• Two references (complete the reference forms, in the application, with contact information)
• Select top three labs and projects of interest from the list below.
• Deadline for receipt of applications is February 1, 2023.
• Deadline for receipt of recommendation letters is February 4, 2023.
• Program contact: cmathis@jhu.edu

Eligibility:

• U.S. citizens, permanent residents, and U.S. nationals, are eligible to apply.
• International students, who are permitted to work in the United States, are eligible to apply.
• College Sophomores or Juniors preferred
• Major in computer science, engineering, mathematics, chemistry, biology, and/or biophysics
• Available during the program dates, June 5, 2023 - August 11, 2023.

If accepted, students on the quarter system can request to take their final exams early or request have final exams proctored at Johns Hopkins.

Interest in graduate school

While not required, we seek candidates with some combination of experiences in scientific or academic research, C++/Python/*nix/databases, software engineering, object-oriented programming, and/or collaborative development (git)

**Students graduating before the start of the program are not eligible for the REU and are encouraged to apply to our RaMP Program.