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NAOMI Version Upgrade

Simon Brocklehurst smb at bioch.ox.ac.uk
Mon Jul 31 06:43:44 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 2.10a is available _now_ via
anonymous ftp from:


in directory pub/smb/naomi/

Academic and commercial upgrades from Version 2.10 will work with current main 
license keys and any existing "feature" license keys.  Users of earlier
versions than 2.10 will need new license keys to allow the upgrade to work.

Upgrade features requested additional facilities for analysis of hydrogen
bonds and chain-breaks.

See the World Wide Web NAOMI site at:


for more details of the program.

What is NAOMI?

NAOMI is a computer program aimed at both specialist and non-specialist
researchers who make use of three-dimensional structures of proteins 
in their work.

The general features offered by the program make it it a useful addition to
programs such as X-PLOR for performing structure-function related 
computations on protein structures. In addition, a number of specific 
types of calculation are offered which are of interest to groups of people.

NAOMI provides interfaces to the graphics programs MOLSCRIPT, INSIGHT II
and QUANTA, as well as its own graphical output, to allow efficient 
visualizations of the results of calculations and analyses. It is 
operated by an intuitive command language, coupled with interactive 
documentation, that allows the user to perform manipulations of and 
calculations on three-dimensional structures of proteins in a 
time-efficient manner.

Features include:

    General structural analysis
    Interfaces to computer graphics programs (MOLSCRIPT, INSIGHT II, QUANTA)
    Dealing with problematic pdb files
    Simulating dynamic properties of proteins
    Prediction of protein function from 3-D structure
    Protein Engineering and Design
    NMR structure refinement
    Tertiary structure prediction
    Prediction of protein folding pathways

NAOMI is Copyright Simon M. Brocklehurst 1992-1995.

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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