From chemistry-request@www.ccl.net Tue Nov 14 18:41 EST 1995
Message-Id: <9511142319.AA21218@scripps.edu>
Date: Tue, 14 Nov 1995 15:18:53 -0800
From: David Case 
To: chemistry@ccl.net
Subject: CCL:New version of NAB now available

ANNOUNCE: version 1.1 of the NAB molecular manipulation language now available.

Tom Macke and David A. Case

We have developed a new approach to the modelling of nucleic acids that is
implemented as a computer language called NAB.  The method was
primarily designed to construct models of helical and non-helical nucleic
acids from a few dozen to a few hundred nucleotides in size, and uses a
combination of rigid body transformations and distance geometry to create
candidate structures that match input criteria.  The language is designed
to provide a flexible way to described nucleic acid structures at an atomic
level of resolution, and contains built-in connections to the AMBER
molecular modelling package, the MEAD programs to compute solvation effects
at the Poisson-Boltzmann level, and the AVS visualization system.

NAB is a computer language (specified through lex and yacc) that allows
nucleic acid structures to be described in a hierarchical fashion, using a
language similar to C or awk, but designed especially for the manipulation
of nucleic acid structures.  We have applied NAB to duplex- and triplex- and
tetraplex DNA, to RNA hairpins and pseudo-knots, to closed-circular DNA, and
to models of recombination sites.  Prospects and progress toward
implementation of these methods to larger systems (such as tRNA, the
hammerhead ribozyme, and the Group I intron) look positive.  This language
may also be useful for other molecular modelling tasks, and a protein
library is included in the distribution.  NAB can also be used as a general-
purpose language for writing programs that deal with three-dimensional
biomolecular structures.

New features in version 1.1:

-- better distance geometry performance
-- better error messages
-- new molecule attributes
-- support for peptides and proteins

NAB can be obtained from ftp://ftp.scripps.edu/pub/macke/nab5.v_1_1.tar.Z.
Send questions/comments to macke@scripps.edu.