[modeller_usage] Multi-domain protein modeling

["bestkarollo" <>]

       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