Hi all,
I'm trying to dock some peptide candidates to a pocket. The pocket of template complex has a 6 aa length peptide , XXXpSXXX. But my peptide candidates I would like to dock is 7 aa length, XXXXXSXX. As you see, the phosphorylation site between substrate and docking peptide don't match on the same position.
My question is
1. Will it be a matter of the enenry score (specially I_sc, pep_sc, etc) if the peptide I would like to dock is longer than the template? if yes, what's the best solution for this case?
2. Will it be a matter of the enenry score (specially I_sc, pep_sc, etc) if the phosphorylation site(where I constraint) of the peptide candidate don't match the same position of the template? if yes, what's the best solution for this case?
Thank you!