haddock gives many clusters and in each cluster there are 4 structures. i am going to chose cluster which has lowest z score. but i am confused from it has four structures so which structure i should select . am i going in right direction?
i am doing protein peptide docking. I gather the information about active and passive residues from CPORT. Is this information valid?
Please help me what i should do with haddock results .
You should at least look at all clusters that are close to each other considering the haddock score
And within one cluster the first model would have the best score. But again the ensemble might give you a better picture of how well defined the solution is
by haddock score you mean to say consider those clusters that have low haddock score.
what is meaning of z score here in each cluster?
It’s a classical z-score calculated from the score of each cluster.
Use the haddock score
then i should choose the cluster with least haddock score. from that cluster first structure has least binding energy.