Summary
In this second part of the course you have learned;
- How to sample solvent and ligand conformation using rigid body translation and rotation moves
- How to sample the internal (bond, angle and dihedral) degrees of freedom of the ligand and protein sidechains using internal moves
- How to sample the protein backbone using backbone moves
- How to combine a collection of moves together into a weighted set that can be used to perform balanced sampling of a solvated protein-ligand complex
What Next?
Now you know how Monte Carlo works, you can be more confident using software and methods that are based on Monte Carlo sampling. Such software includes Sire, ProtoMS, BOSS / MCPro and MCCCS Towhee.
Monte Carlo has many applications. These include;
- Calculation of relative protein-ligand binding free energies. An easy-to-use interface for these calculations based on the ligandswap method is provided with Sire. Software and instructions on how to do this are provided here.
- Calculate of absolute protein-ligand binding free energies. An easy-to-use interface for these calculations based on the waterswap method is provided with Sire. Software and instructions on how to do this are provided here.
- Calculation of the difference in free energy between molecular mechanics and quantum mechanics models of molecules. Again, an easy-to-use interface for these calculations is provided with Sire. Software and instructions on how to do this are provided here. In addition, this self-guided workshop will teach you the theory and methodology behind these calculations.