ANNOUNCEMENT: version 5 of the NAB (Nucleic Acid Builder) molecular
manipulation language is now available
Thomas J. Macke, W.A. Svrcek-Seiler, Russell A. Brown and David A. Case
NAB was originally designed as a small modeling language (a "molecular awk"),
with a principal focus on constructing models for non-helical nucleic acids.
It has been used to construct models of helical and non-helical nucleic acids
from a few dozen to a few hundred nucleotides in size, and provides a
combination of rigid body transformations and distance geometry to create
candidate structures that match input criteria.
As the code developed, an implementation of the AMBER force field was added,
which includes a version of the generalized Born model for solvation effects.
Version 5 adds analytical second derivatives, opening the way to new types of
simulations. Force-field calculations can be carried out on proteins and
small molecules, as well as nucleic acids, making NAB a useful platform for a
variety of modeling tasks. For example, NAB code is incorporated into both
AutoDock and Dock to perform force-field calculations on protein-ligand and
nucleic-acid-ligand complexes.
NAB consists of a language specification (constructed using lex and yacc) that
has special support for macromolecules and their components, along with more
general-purpose constructs such as strings, regular expressions and hashed
arrays. This language has a C-like syntax, and is compiled to C code at an
intermediate stage. There is also a support library (primarily coded in C)
that implements rigid-body transformations, distance geometry, energy
minimzation, molecular dynamics and normal mode analysis.
Version 5 is a major update and consolidation. It makes better connections to
the Amber suite of programs, and implements for the first time second
derivatives of the generalized Born solvation model. Force field calculations
can be carried out in parallel on machines that support OpenMP.
NAB is distributed as source code under the GNU General Public License (GPL).
It runs on Linux, Mac OSX, Windows (under cygwin), and on most flavors of
UNIX. For more information, and to download the code, please visit our web
site:
http://www.scripps.edu/case
and click on the "NAB" link in the left-hand menu.
We encourage NAB users to contribute to the code, or to help us integrate it
into other environments. Please contact Dave Case, <case "at" scripps.edu> if
you wish to help out.
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Received on Fri Apr 08 2005 - 18:53:00 PDT
