Sukanya obtained her undergraduate degree in Chemical Engineering from Indian Institute of Technology, Kharagpur in India where she worked on developing droplet-based microfluidic devices for studying protein aggregation. She did her PhD from University of California, Berkeley. Her dissertation research was on understanding intrinsically disordered proteins, in particular the Alzheimer’s amyloid-beta peptide and amyloid fibril aggregation using all-atom and coarse-grained molecular dynamic simulations. In the Mobley lab, she is focusing on using molecular simulations and modeling to better understand protein-ligand interactions. Her projects are listed below-
1) Predicting the probability of different binding modes for flexible ligands using an non-equilibrium candidate Monte Carlo method (BLUES)
2) Structure based drug design using a combination of docking and binding free energy methods for protein targets. This work is in collaboration with Prof. Jefferson Perry at UC Riverside.
3) Predicting protein-ligand binding poses and binding affinities for the 2018 D3R grand challenge .
4) Calculatingwater/1-octanol and water/hexadecane partition coefficients for small molecules using alchemical free energy calculations. Anh Nguyen, an undergraduate in UC Irvine is working on this project.
5) Predicting free energy differences between different loop conformations.