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Jacob

MD/PhD Doctor of Medicine and of Philosophy candidate

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

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

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