ANNOUNCE: NMR structure refinement

Simon Brocklehurst smb at
Wed Aug 23 08:33:20 EST 1995

NAOMI - Module Announcement

(Please note, NAOMI is provided at zero charge for academic use)

(e-mail contact smb at

The NMR structure refinement module of NAOMI is available now.
It allows hydrogen bond restraints to be "sorted out" objectively,
and automatically.

Existing users should request a FEATURE 5 license key, and upgrade
to Version 2.10c of the program.

An extract from the User Guide is shown below:

Hydrogen bond restraints are important in defining the three-dimensional
structure of proteins in many NMR structure determinations. But it is 
difficult (and often impossible) to identify hydrogen bonding partners by
direct observation by using current NMR experiments.

One of the best ways to attack this problem is to analyse ensembles of
structures calculated without hydrogen bond restraints, to see where
donor-acceptor pairs can be identified unambiguously. In combinatation with
hydron exchange NMR experiments, this approach can, in favourable cases allow
identification of both donor and acceptor partners of:

     both regular and distorted secondary structural hydrogen bonds.
     main-chain - main-chain tertiary hydrogen bonds
     side-chain - main-chain hydrogen bonds involving amide-proton donors


See the User Guide on NAOMI WWW site at:

for more details and example output.

NB NAOMI 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 | WWW:

More information about the Bio-soft mailing list