IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP

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.

    mutate 14 A
    mutate 15 K
    mutate 16 H

  Look at:




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

   repair side-chains

   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/ 

More information about the X-plor mailing list

Send comments to us at archive@iubioarchive.bio.net