Hello,
I am modeling a structure composed of two modules: M1 (one domain) linked to M2 (two domains). M1 - 100 residues M2 - 200 residues
First, separately I generated models for M1 and M2 and I joined them. Secondly I generated models for M1 and M2 in this way that they have been already joined - I created one chain with already joined M1 and M2. I separated M1 and M2 and I compared DOPE scores.
Models modeled "alone" had better score: M1 = DOPE = -9360 M2 = DOPE = -20497
than models after "separation"
M1 = DOPE = -9129 M2 = DOPE = -20211
1_Does a difference in DOPE score is significant ? 2_Which models chose ? 3_Which modeling procedure is in better agreement with protein folding problem? Domains fold indepedently but from the other hand a final structure is composed of two joined elements = energy of "final protein" should be influenced by energy of M1 and M2 - so maybe despite worse DOPE scores a chain modeled with already joined domains is "much" biologic.
Yours sincerely,
Karol Kaszuba