I have some questions about Molecular Docking Method in DS.
1) If you have any protein and various ligands. Firts of all, how do you determine or find the binding site of the any protein both ways (experimental and theoretical) in Discovery studio.
In addition, which condition(s) do you add water or not to calculate the protein-ligand or protein-protein interactions by using docking method?
2) There are different Docking approaches, such as protein is rigid and ligand is flexible or both of them are flexible... etc.
Could you give me advantage or disadvantage of these approaches and How can I apply flexible docking in DS software, please send me detail informations and sources about it?
Thanks
Tuğba
