Excluding some proteins (PDB IDs) from the structural similarity search in EvoDesign tool?

Dear lab member,

I would like to know if one can we exclude specific PDB IDs from the structural similarity search carried out in the EvoDesign system.
If true, then what steps we must follow to get it done.
On other hand, I would like to know if exists and standalone version of the EvoDesign Framework.

Many thanks in advance,
Ernesto