The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to http://www.bonvinlab.org/software/haddock2.2
I am trying to dock a protein domain (Protein 2) to a site on another protein containing a flexible loop (Protein 1). I would like to get an idea about the favourable conformations of the loop for protein-protein docking. In order to do so I tried the following.
a) Creating an ensemble of cluster representative conformations(12 representatives) of protein 1 with different loop conformations and then using this ensemble to dock protein 2 on it.
b) Individually docking each conformation of protein 1 with protein 2.
The restraints used were exactly same for all the calculations.
I have following queries regarding results.
- Is it possible/correct to compare the results of 12 separate runs considering that the restraints etc were exactly same for all the runs with only difference being conformations of protein 1?
- Is it possible to combine the results of these 12 runs and score the complexes again? If yes, how?
- Would increasing the conformational sampling in approach (a), provide a better idea about the relative preference of certain conformation as opposed to approach (b)?
- *rmsd.disp file is missing in the downloaded results for most of the runs. Is there a way to calculate RMSDs for the complexes to perform clustering using different cutoffs?