Jacob A
- Research Program Mentor

MD/PhD candidate at Harvard University

Expertise

Structural Biology, Cryo-EM, Cryo-ET, Ligand Docking, Chemical Biology, Bioinformatics, Computational Biology, In Silico Screening

Bio

I completed my undergraduate studies at the University of Michigan in Ann Arbor. There, I focused on single molecule fluorescent imaging. I also worked at the NIH on hydrogen exchange of backbone amides using NMR. I now work on determining protein structures using electron microscopy as part of dual MD-PhD training. In spare time, I enjoy reading about the history of science and biographies/memoirs of scientific figures. I like to run, hike, and follow Michigan sports (football, basketball especially!).

Project ideas

Project ideas are meant to help inspire student thinking about their own project. Students are in the driver seat of their research and are free to use any or none of the ideas shared by their mentors.

SARS-COVID-19 Protease Inhibitors

Since the pandemic began, a race was on to find inhibitors of the main protease of conornavirus. Several structures of the protease have been solved with fragments in the active site. Beginning with a literature review on proteases, one could look at the cornavirus proteases (MERS, SARS, SARS-COVID-19) for structural differences. Analysis of the fragments bound to the crystal structures of SARS-COVID-19 protease may inform future rational efforts for protease inhibitor design.

CAR-T Targets

CAR-T cells are cells engineered to identify cancer cells and, through several mechanisms, lead to decreased cancer burden. Reviewing the mechanism of CAR-T cells and technology developments, we can propose a new CART-T cell target antigen and describe its process of research, development, and manufacture.

Processing Available Cryo-EM Data

There are many open source datasets of images available that have been used to determine atomic structures of particles. A general idea might be to reprocess this data with different techniques/software to answer questions that have not yet been answered. This would be computationally expensive. Likely will require access to a computer with a strong GPU.

Coding skills

Python, C++, Matlab, R

Languages I know

Urdu/Hindi, intermediate

Teaching experience

Mentored high school students in research internships. Taught introductory neuroscience workshops at the high school level. This involved laboratory based instruction in dissection, anatomy, and neuroscience (action potential, receptor biology). I facilitated and taught study groups in organic chemistry, animal physiology and neuroscience, and general chemistry at the University of Michigan. Chalk talk to undergraduates at Wellesley college on comparative structural biology techniques. Premedical advisor at Harvard college.