Critical Assessment of PRedicted Interactions (CAPRI) has specific criteria for ranking the protein complex predictions. These criteria are :
1- 'fnat' "the number of nativeresidue–residue contacts in the predicted complex divided by the number of native contacts in the target".
2- L-rms "is the backbone root-mean-square displacement of the ligands in the predicted versus the target structures".
3- I-rms, "is the root-mean-square displacement of thebackbone of the interface residues only, in the predicted versus the target complexes".
I am looking for a tool (or a script) which can take a .pdb file of a protein complex and analysis it based on CAPRI criteria and output the three main criteria. Do have any suggestion?
Thanks for you help.
reference:  "Assessment of Blind Predictions of Protein–Protein Interactions: Current Status of Docking Methods".Mendez et. al. PROTEINS: Structure, Function, and Genetics 52:51–67 (2003)