Build a QSAR model for SARS-COV-2 with public data or your local data, The model molecular descriptors as independent variable, bioactivity as dependent variable, random forest as amathematical model.

Starting from a PDB bank structure or a local PDB structure, setting up and run a molecular dynamics simulation with user-friendly in mind, with Ambertools and OpenMM, by mostly clicking the mouse

Prepare a molecular dynamic simulation from scratch without installing local VMD, use LigParGen for topology, it is one of the most reliable MD for a general solution protein-ligand simulation.

Calculate the binding free energy difference between two small molecules against the same protein target. This is one has cost me quite some time, also one of my favorate repositories.

Absolute binding free energy of protein target with a bound small molecule. Inspiration comes from a combination of Justin's Gromacs tutorial and the Gromacs-2016 Alchemical simulation tutorial.