with Prof. Greg Bowman Identification of cryptic pockets using AI mediated molecular dynamics simulationsSkills: Markov State Model · Biophysical Chemistry · Molecular Dynamics

with Prof. Greg Bowman ★ Interaction of protein with lipid bilayers using molecular dynamics simulation and Markov state modelling ★ Understanding conformational heterogenecity of Plasmepsins (focusing on plasmepsin-V)Skills: Python (Programming Language) · Markov State Model · Molecular Dynamics

★ Wrote a critical review which highlights several aspects of pepsin-like aspartic proteases which can bring together biomolecular simulation and biophysical experiments. Paper here: RSC Adv., 2021,11, 11026-11047

★ Used funnel metadynamics and distance restraint along solvation degrees of freedom to accurately predict host-guest binding free energy in SAMPL5 challenge. We found out that long-lived water molecule in haste cavity affects ligand binding. ★ We hypothesised that the conformational dynamics especially flap opening in pepsin-like aspartic proteases such as plasmepsin-II, BACE-1 is governed by side-chain flipping of conserved Tyr. This study shows conformational heterogeneity of protein side-chains and its effect on ligand binding. ★ Used second order independent component as order parameter (parallel-tempered metadynamics) to capture transient loop opening in basic pancreatic trypsin inhibitors and proposed a new mechanism of hydrogen-deuterium exchange (HDX).

✣ Performed MD simulation, PCA and residue interaction network to understand how mutation affects conformational dynamics of HIV reverse transcriptase inhibitor ✣ Deciphered the role of PR20 mutations in HIV-1 protease and their role in conformational dynamics using computational microscope, molecular dynamics simulation. ✣ In collaboration with researchers from KU, Leuven, repurposed HIV-1 protease inhibitors on dengue and chikungunya virus and discovered that Nelfinavir has mild activity against these viruses.

✣ Co-founded "Open Source Drug Design and In-Silico Molecules" (2010-15) ✣ Synthesised Methyl-4-(ethoxymethyl)-benzoate ✣ Mentored multiple undergrads in the field of computer aided drug design

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