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OS: Linux, ...

License: Freeware, Registration

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. We have applied NAB to duplex-, 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.

As the code developed, an implementation of the AMBER force field was added, which includes the AMBER implementation of the generalized Born model for solvation effects. Version 5 includes 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 provide a mechanism to carry out force-field calculations on protein-ligand and nucleic-acid-ligand complexes.

It is now bundled as a part of AmberTools