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 2.4 is available as of now from the
NAOMI Web site at:
or via anonymous ftp
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).
New features in upgrade:
In main module:
New fully automatic interface to RASMOL
Wild-card selection of residues
Automated identification of interior and exterior residues
new "protwrite" command for outputing protein-level
In the NMR module:
New prediction of NOEs from structure command
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
automatic 'key' residue identification
automatic hydrophobic core/packing analysis
automatic hydrogen bonds main-chain and side-chain
identification (including high quality energy
automatic secondary structure (helix, strand and turn) classification
using fuzzy logic
automatic supersecondary structure classification (beta-hairpin
conformational parameters: phi,psi,chi1,chi2,chi3,chi4,chi5 etc
solvent accessibility (both absolute and percentage) calculations
automatic identification of disulphide bonds, salt bridges,
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),
RASMOL, INSIGHT and QUANTA to allow automatic preparation of
figures and time-efficient visualization of structures.
More details are available on the Web site.
NB NAOMI currently works only on Silicon Graphics workstations running
IRIX 5.* or IRIX 6.*
|| ,_ o Simon M. Brocklehurst,
| / //\, Oxford Centre for Molecular Sciences, Department of
| \>> | University of Oxford, Oxford, UK.
| \\, E-mail: smb at bioch.ox.ac.uk | WWW: