Overview of my research:

Cryptic Binding Site of Proteins

We have found unique side-chain fluctuations of cryptic binding sites via molecular dynamics simulations.

Our paper 👉 "Structural Fluctuations of Aromatic Residues in an Apo-Form Reveal Cryptic Binding Sites: Implications for Fragment-based Drug Design"

Source code to analyse the fluctuations 👉 github

Intrinsically Disordererd Protein

We have explored the structural ensemble of an intrinsically disordered region, p53 C-terminal domain, via a generalised ensemble molecular dynamics simulation. We have identified various binding modes on a target protein.

Our papers 👇

1. "Variation of Free-energy Landscape of the p53 C-terminal Domain Induced by Acetylation: Enhanced Conformational Sampling"

2. Multimodal Structural Distribution of the p53 C-Terminal Domain upon Binding to S100B via a Generalized Ensemble Method: From Disorder to Extradisorder

SARS-CoV-2 main protease

We have investigated monomeric and dimeric states of the SARS-CoV-2 main protease, identifying water molecules that can be crucial to keep the dyad configuration.

Our paper 👉 Asymmetric dynamics of dimeric SARS-CoV-2 and SARS-CoV main proteases in an apo form: Molecular dynamics study on fluctuations of active site, catalytic dyad, and hydration water