Protein loops

Simon Brocklehurst smb18 at
Tue Jul 20 13:28:06 EST 1993

Hi Chris,
      If I understand your problem correctly you want to look at a protein
structure minus one loop say, and then have the computer go away and work
out the "best" sequence for the loop by taking into account the remaining
protein surface.
      If that were the "real problem" so to speak, then this would not be
too difficult to do.  However, the reasons why particular loops have particular
sequences is not just to do with intramolecular protein-protein interactions.
In particular, intermolecular protein-solvent and protein-protein interactions
have to be taken into consideration and I think this is where the difficulty
in selecting the "best" loop sequence comes.  I don't think this is a 
tenable problem at present, but if you can think of a way of doing it, let me


Simon M. Brocklehurst
Cambridge Centre for Molecular Recognition
Department of Biochemistry
University of Cambridge
Tennis Court Road

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