Computational Chemistry
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NAB
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.
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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