Actually, the scaffold is entirely different from the native scaffold.. I am trying to bring the native scaffold topology to my protein, which is Green Fluorescent Protein. So, far I have modelled the structure with minor changes of 2 or 3 residues in the scaffold, keeping in mind the topology of the original active site.
I did not understand the concept about designing substrate/product hybrid structure, coz in the tutorial only TS modelling has been described.
Also , I did not understand much about – “You then need to prep your starting structure – align your hybrid molecule in the appropriate starting location (the key thing is to get the constrained geometry correct – don’t worry too much about clashes with sidechains, as the enzyme design application should fix those) and place the appropriate remark lines at the top of the PDB, telling which amino acids correspond to which constraints.” Can you explain it a bit ??
For your information , I already have the predicted and published constraints for bond length, dihedral angles. So, now I want to know that what all constraints are there if I simple apply will that be ok, say for eg. in the native protein cys17 makes h-bond with phosphate of p-Tyr, but after docking I found that the h-bond is not present. So, can that be modelled as a constraint or not ??