Binding of the first ligand to the protein can affect binding of the second ligand (of the same or different kind): the first ligand can change the conformation of the binding site for the second ligand, or itself become a part of the binding site for the second ligand. The binding of the first ligand can inhibit or enhance the binding of the second ligand.

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What can be predicted using the multiple docking approach? The structure of the complex of the protein with multiple ligands, but only if the protein structure is not altered by the ligands or if the protein structure is available in the ligand-induced conformation. The structure may help explain experimental observations (see Figure 6 in the paper below).

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Prokop et al. (2003) J Biol Chem 278: 45094-45100.

https://www.ncbi.nlm.nih.gov/pubmed/12952988