I would like to test the ability of some docking programs and my own one to predict the binding site of different ligands on the same protein. For that purpose I was reading literature in order to find examples of proteins where depending on the ligand, it bind in one part or another of the protein. But I found nothing relevant at the moment. I wonder if you know such databases or can you point to some examples from literature or wherever
I think you are looking for datasets for docking benchmark.
In this case, I can't give a specific answer without the details about your docking program. If I were you, I would look at recent manuscript that describe docking programs similar to your program and use one benchmark data from them.
- If your docking program deals with protein-small molecule docking
See: http://zlab.bu.edu/zdock/benchmark.shtml ZDOCK is one of my favorite docking program. I think this dataset should be a good start. * You can also look in to co-crystallized protein-ligand complexes. For example browse PDB for tyrosine kinases co-crystallized with peptide substrates... etc.
- If your docking program deals with protein-DNA docking:
- If you docking program deals with protein-protein docking