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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?

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Huameng Li and Chenglong Li have done multiple ligand docking in two (AFAIK) of their works:

  1. Multiple ligand simultaneous docking: Orchestrated dancing of ligands in binding sites of protein
  2. 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.

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  • $\begingroup$ I thank and appreciate [WYSIWYG] for your wonderful answer. I have referred the both articles before, but there is no proper protocol for applying the problem in the AutoDock. $\endgroup$
    – ak-SE
    Dec 17, 2014 at 7:29
  • $\begingroup$ Perhaps you can see this paper. They talk about implementing automated docking and this is referred by Li and Li. $\endgroup$
    – WYSIWYG
    Dec 17, 2014 at 8:33

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