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NAOMI
home software section
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.
Upgrade features
Upgrade features : Side-chain manipulations now include hydrogen
atoms where appropriate. This makes for more seamless integration with
X-PLOR (e.g. for molecular dynamics simulations, energy minimization,
NMR structure calculation etc after manipulation of protein
structures using NAOMI).
Configuration
NAOMI currently works only on Silicon Graphics workstations running
IRIX 5.
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).
Simon M. Brocklehurst
Oxford Centre for Molecular Sciences
Department of Biochemistry
University of Oxford, Oxford, UK
E-mail: smb@bioch.ox.ac.uk
Please send your comments and your suggestions to Yves
Epelboin, epelboin@lmcp.jussieu.fr
.
Last update January 04 1996 Y.E.
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