Kevin (Shih-Hsien) Liu

Analysis on the number of non-hydrogen atomic contacts between a ligand and each of specified residues on the protein following molecular docking of multiple ligands to a protein structure.

Bash shell scripts that process GROMACS files for automating a series of molecular-dynamics (MD) simulations on NERSC supercomputer.

The simulated annealing algorithm that minimizes a cost function, which indicates the degree of matching between the force field (FF) and density-functional theory (DFT).

Ranking of all the ligands in molecular docking by their AutoDock Vina scores, an approximation to their free energy of binding to the protein.