Desolvation Energy

Hi! I am working with protein-protein docking, I got an acceptable score (negative) for the rest but my desolvation energy is still positive, I mutate my defined residues into non-polar (e.g. cysteine) to confirm if it is an active residue and run the docking again and surprisingly I am now getting negative desolvation energy. Questions:

  1. What are the alternatives to achieve a negative desolvation energy without mutating my protein?
  2. Is my restraint (defined active residues) the problem why I am getting a positive desolvation energy?

The desolation energy can indeed remain positive … This is an empirical energy term.

Burying charges is usually bad.

Hello, Professor. In the HADDOCK result, where can these Burying charges be found? is it the Buried Surface Area?

I mean charged amino acids at the interface of your complex.

My protein professor is proven to have a high amount of small and charged residues resulting in their intrinsically disordered nature. Is it reasonable if my complex has charged amino acids in its interface because of this fact?

There is no right and wrong answer to that one…

But IDPs indeed often use quite charged amino acids.