I am doing a project on protein-protein docking. My objective to test how good a docking algorithm is. For this I will be doing unbound docking of hetero-dimeric proteins. For every hetero-dimer, I have multiple unbound structures for each of the 2 chains. How do I select 1 unbound structure from the multiple options ?

This is my strategy: i. I would look for highest sequence similarity between the bound and unbound structures ii. In case of tie in step i, I would look for the structure with least number of missing residues in the interface area.

Any other factors for me to consider?