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.