[gmx-users] Refolding modeling

[egorov]

Hello gmx-users,

Suppose, we have a protein that may change its folding upon ligand
binding. We have not possible template for this process from other
homologues proteins and dont know what kind of ligand may be here.
What we can do in this situation?
May be, first step is in identification of flexible and rigid regions in the
protein by means of such kind of programs as DomainFinder. An then use
some force influence on such sites by some technics from Molecular
Dynamics? And if yes, what this technics is?
  
Thank you very much for your attention and suggestions.
-- 
Best regards,
D. Egorov,
Ural State Medical Academy.