Since there is confusion in selecting a target site with correct PDB ID for molecular docking of drugs. E.g. 3-CL protease has lot of PDB ID, Which one to select?
Choosing the PDB for your protein of interest depends on factors like Resolution and the number of missing residues. In case of residues missing, you have to model it. And to know about the target site/active site, literature mining and some prediction tools can be helpful and used.