Subject: ANNOUNCE: version 4 of Nucleic Acid Builder released

From: David Case <[email-masked]>
Date: Wed, 22 Sep 1999 08:22:34 -0700 (PDT)

ANNOUNCEMENT: version 4 of the NAB (Nucleic Acid Builder) molecular 
   manipulation language is now available

Thomas J. Macke and David A. Case

We have developed an 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 several levels of
resolution, and contains built-in implementation of the AMBER force field, a
generalized Born model for solvation effects, and a link to 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 molecular 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 the small subunit of the ribosome and of recombination sites.

NAB contains connections to the Amber and YAMMP modeling programs and force
fields.  This means that NAB programs can run analysis (including
minimization and molecular dynamics simulations) using either the all-atom
force fields from Amber or the reduced representation nucleic acids models
>from YAMMP.  The generalized Born solvent model is also included.

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 4:

-- (initial) support for low-resolution nucleic acid modeling
-- better distance geometry performance
-- better error checking and debugging facilities
-- expanded molecular mechanics options, including generalized Born terms

NAB is distributed as source code via anonymous ftp.  It runs on many
flavors of UNIX (IRIX, Linux, Solaris, HP-UX, Digital UNIX) and on
Windows 95/98/NT.

Details at: http://www.scripps.edu/case.
FTP site:   ftp://ftp.scripps.edu/pub/macke/nab-4.0.tar.gz

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David A. Case                     |  e-mail:      [email-masked]
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  WWW:                         
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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