Doubt on docking

Question

[Ria]

I need to know how to find active site of a protein for docking. What site to use and how? I need to know how to find x, y, and z coordinates so i can give as grid coordinates while docking.

Answer 1

[Mensur Dlakic]

I think you are wrongly assuming that we can help you with this without knowing what is the protein of interest.

A general answer is that you first must know the active site and residues around it. Then you can open a PDB file and find one of those residues that are closer to the surface, and find coordinates for its Calpha atom. That should be a good approximation of the active site for docking, especially if you pick a cube that is at least 50 angstroms in all directions.