I have performed two different
HADDOCK2.2 calculations, one discarding for each docking trial 50% of the
restraints at random as default, and a second calculation where I have
turn off this option. The results are completely different
highlighting that perhaps I have some errors in my input data. In
both calculations ”active”
residues of protein A were derived from NMR data while, in absence of the chemical
shift assignment for the NMR signals of protein B, I applied CPORT to predict
active residues of protein “B”.
When I exclude the 50% of the
restraints at random, I obtain that only 67% of the HADDOCK structures
are clustered in 29 clusters while when I turn off such option I obtain
that 97% of the structures are clustered in 4 clusters! but in the latter
case the HADDOCK score is much higher ( positive values) than in the first case
and the Restraints violation energies are four time those obtained in the case
when I have excluded the 50% of the restraints.
In the structures of the adducts obtained
without excluding any residues, the orientation of the protein B is similar in
the four clusters and the residues of B involved in the interaction are
almost the same (those derived from PINUP predictors), but there are some “active”
residues of protein B that are not involved in the interaction at all; they are
therefore not satisfied. Such residues derived all from the prediction of one
of the predictors of CPORT. I think that this is the reason why I have an
increase in the Restraint violations energies.
My question is, do you think that turn
off the option that excludes the restraints at random is correct? ,
Which is the output file that provides a list of the restraints that give violations? I was thinking it was “ana_noe_viol_all.lis” file but I do not have this file in my dyrectories. Do I need to generate it with the script .ana_noe_viol.csh ?
How can I improve my calculations? Do you think it is correct exclude some residues, for example those predicted from CPORT that are not satisfied in the calculations?
Thanks for your suggestions