I’ve used the FlexPepDock server to dock a small peptide of 8 residues into a homology model I’ve build. Everything went fine but I’ve become worried by the total score that seems to be a big positive number. The data.txt is this:
I’m guessing that the score shows that the position is not suitable for the docking. I had already put the peptide inside the site where it should be located. Am I right? Should I correct anything? How could I explain this numbers?
Thank you in advance.
total_score as high as in this case is really not expected. What do you see in other scoring terms like I_sc, pep_sc; are they also very high? May be you guess is right. Could you provide the job ID or upload the input file so that I can have a look into it.
This could be due to an internal clash in the receptor that is either due to backbone clashes (that are not relieved since classical FlexPepDock optimizes only the side chains on the receptor side), or due to side chains that clash (if you did not prepack).
In any case, you should check the interface score and the peptide score to make sure these are negative.
You can also look at the output pdb structure. After the coordinates you will see a listing of energy values for each residue. This can allow you to pinpoint the residue with clashes (bad total score and bad fa_rep).