NAOMI

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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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