Making a New Structure?

Simon M. Brocklehurst smb at bioch.ox.ac.uk
Mon Apr 29 05:46:56 EST 1996


Todd Charles Wood wrote:
> 
> I am looking for a program that will read in PDB coordinates of
> the backbone of a protein and build onto that the sidechains
> that I specify.  I want to use this "new" structure to do
> energy minimization on.  Any suggestions?
> 
> Todd Wood
> tcw3r at virginia.edu

   NAOMI might do what you need - to give you an idea, here's how
you would build the sequence A K H at residue positions 14, 15 and
16 in the protein fold.

    tyra
    mutate 14 A
    mutate 15 K
    mutate 16 H
    end

  Look at:

    http://www.ocms.ox.ac.uk/~smb/Software/N_details/naomi.html

  and:

    http://www.ocms.ox.ac.uk/~smb/Software/N_details/examples/side-chains.html

  If your backbone coordinates have the right amino acid residue sequence
  in the PDB file, you could instead use the command:

   tyra
   repair side-chains
   end


   which would do everything in one go.

_____________________________________________________________________________
|
|  ,_ o     Simon M. Brocklehurst,
| /  //\,   Oxford Centre for Molecular Sciences, Department of Biochemistry,
|   \>> |   University of Oxford, Oxford, UK.
|    \\,    E-mail: smb at bioch.ox.ac.uk | WWW: http://www.ocms.ox.ac.uk/~smb/ 
|____________________________________________________________________________



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