If I have a homodimerized protein .. in particular the crystal structure of which. and my ultimate target is to inhibit such dimerization. so i have designed a couple of covalent inhibitors at the an essential proint of contact, i have also conducted v-HTS at the most essential point of contact between the two monomeric protein domains.

now i am quite confused .. what do first and how to do it?

should i try to redock the two proteins and acquire the binding energy and compare that with the ptn-lgnd complexes, or calculate the binding energy directly from the crystal structure (which i don't really know if feasible for ptns?)... or try to redock the ptn-lgnd complexes against one another .. I just don't know what do at this point.

Any guiding remarks would be earnestly appreciated, thanks in advance!