Hi;
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"[1].
2- L-rms "is the backbone root-mean-square displacement of the ligands in the predicted
versus the target structures"[1].
3- I-rms, "is the root-mean-square displacement of thebackbone of the interface residues only, in the predicted versus the target complexes"[1].
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: [1] "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)
Did you try contacting the CAPRI judges? They must have written a script for this already. Here is their contact info: http://www.ebi.ac.uk/msd-srv/capri/management.html I have emailed them before and they are fairly quick to respond.
Yes I have. They mention that the toll is not publicly available. although they helped me to process some of them but I need to develop myself for long term use.
Hello, I saw your question. And I kind of have the same question. did you figure out how to assess the protein-protein Docking output according to the CAPRI criteria? Would be really helpful to hear from you.