Is it possible to dock multiple ligands with a target? If so, what is the suitable software used for? -- Is it possible to fix specific docking region for the target (or) automatic?
Huameng Li and Chenglong Li have done multiple ligand docking in two (AFAIK) of their works:
- Multiple ligand simultaneous docking: Orchestrated dancing of ligands in binding sites of protein
- Drug Design Targeting Protein–Protein Interactions (PPIs) Using Multiple Ligand Simultaneous Docking (MLSD).....
The method is called Multiple Ligand Simultaneous Docking (MLSD). I am not at all an expert in this field and you should read the first paper for details on how they implemented this. This algorithm was implemented on AutoDock.