Scholar Link: Chowdhury, Ratul
I am a Postdoctoral Fellow in the lab of Peter Sorger in the Department of Systems Biology and the Laboratory of Systems Pharmacology at Harvard Medical School. I am trying to devise new machine learning strategies to accurately predict the structure of a protein from its amino acid sequence alone. On the application side of things, I am predicting structures of several human voltage gated ion channels and docking a library of drugs to discern non-opioid drug binding modalities.
We have recently contributed towards uncovering the role of ancestral recombination of betacoronavirus strains in making the current SARS-CoV-2 strain highly specific to human infection. We provide residue-level biophysical insight to explain our findings.
I received my PhD in Chemical Engineering from Penn State University, in 2019 under the supervision of Profs. Costas D. Maranas, and Manish Kumar. During my PhD, I developed mixed integer linear optimization tools for redesign of (a) channel proteins to precisely tune the pore size and chemistry for targeted separations and even nanopore DNA sequencing, (b) enzymes for altered substrate and cofactor specificity, and (c) de novo, template-free design of non-immunogenic antibody variable fragments against any target protein (with experimentally validated test case with alpha-synuclein protein responsible for Parkinsons disease). Additionally, I have worked on designing artifical nanopore channels for precise molecular separations and we designed channels that emulate naturally occuring aquaporins and outperform them in terms of ion/ proton rejection. Next, I have worked with designing anti-microbial plant peptides and experimentally demonstrated complete virus removal from contaminated water using inexpensive sand filters embedded with these proteins. One of my final efforts from PhD include devising an optimization protocol to (a) predict amino acid indels along with substitutions for more efficient protein design by using the chain length as a design lever, (b) design a bio-sensor for polyketide synthesis.