We offer this software dealing with validation of protein structures:
Validator DB
MotiveValidator
ValTrendsDB

Validator^DB 

Database of validation results for ligands and non-standard residues in the Protein Data Bank. Read more in NAR.

MotiveValidator  

MotiveValidator is a platform for a set of applications designed to help you determine whether a residue or a ligand in a biomolecule or biomolecular complex is structurally complete and correctly annotated according to its models stored in the wwPDB Chemical Component Dictionary (wwPDB CCD). Read more in NAR.

ValTrendsDB  

is a database of biomacromolecular structure validation trends. Read more in Bioinformatics.