NAOMI Version 2.2

Simon M. Brocklehurst smb at bioch.ox.ac.uk
Mon Oct 2 08:55:27 EST 1995

NAOMI - Version Upgrade Announcement
(Please note, NAOMI is provided at zero charge for academic use)

(e-mail contact smb at bioch.ox.ac.uk)

The computer program NAOMI Version 2.2 is available _now_ from the
NAOMI Web site at:


or via anonymous ftp from:


in directory pub/smb/naomi/

Users of versions older than 2.10 will need new license keys to allow 
the upgrade to work (please contact the author in this case).

Upgrade features : solvent accessibility, symmetry operations, disulphide
bonds, new side-chain modelling commands, new molscript output 
options e.g. see the illustrations on the Cytokines Web:


Fixes of minor bugs in key residues and molscript output commands.

What is NAOMI?

NAOMI is an easy-to-use, state-of-the-art computer program which is 
aimed at both specialist and non-specialist researchers who make use of 
three-dimensional structures of proteins in their work.  It has
hundreds of users Worldwide.

Some facilities offered by the program for working with structure include: 

   automatic 'key' residue identification
   automatic hydrophobic core/packing analysis
   automatic hydrogen bonds main-chain and side-chain 
                   identification (including high quality energy calculations) 
   automatic secondary structure (helix, strand and turn) classification
                   using fuzzy logic
   automatic supersecondary structure classification (beta-hairpin loops)
   conformational parameters: phi,psi,chi1,chi2,chi3,chi4,chi5 etc
   solvent accessibility (both absolute and percentage) calculations
   automatic identification of disulphide bonds, salt bridges, chain-breaks
   side-chain modelling and manipulation 
   applying symmetry operators
   automatic structure repair (building in missing atoms)
   NMR structure refinement module
   interfaces to graphics programs (MOLSCRIPT (and thus Raster3D), 
        INSIGHT, QUANTA to allow automatic preparation of figures

More details are available on the Web site.

NB NAOMI currently works only on Silicon Graphics workstations running 
IRIX 5.*
|  ,_ 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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