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
|| ,_ 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/|____________________________________________________________________________