Subject: new version of NAB available

From: David Case <[email-masked]>
Date: Mon, 12 May 1997 12:42:47 -0700

ANNOUNCE: version 2.1 of the NAB molecular manipulation language now available.

Thomas J. Macke and David A. Case

We have developed a new approach to the modeling 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 implementation of the AMBER force field, a
generalized Born model for solvation effects, 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 and branch migration.

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 molecular structures.

New features in version 2.1:

-- improved users' manual
-- better distance geometry performance
-- better error checking and messages
-- considerably expanded molecular mechanics options

NAB is distributed as source code via anonymous ftp.  It runs on many
flavors of UNIX (IRIX, Linux, Solaris, SunOS, HP-UX, Digital UNIX) and on
Windows 95.

Details at: http://www.scripps.edu/case.
FTP site:   ftp://ftp.scripps.edu/pub/macke/nab-2.1.tar.Z