hydroxyl radical footprinting) to filter the generated decoy structures. known or predicted tertiary contacts (optional)Īdditionally, NAST can use residue-resolution experimental data (e.g. It produces a diverse set of plausible 3D structures that satisfy user-provided constraints based on:Ģ. NAST (Nucleic Acid Simulation Toolkit) is a knowledge-based coarse-grained tool for modeling RNA structures. Please read the instructions posted on the wiki for details.
Nov 09 UPDATE - NAST is now available on most unix/pc/mac platforms. Lots of exciting new features, detailed in the new manual NastTutorial.v4.pdf (under the "Downloads" button on the left).Ĭ2A has been separated from NAST, please download and install separately from the C2A project page: /home/c2a.įeb 2010 UPDATE 2 - If you are running C2A on a molecules that contains an "end" piece of length 1, please see the wiki for special instructions for fixing a bug that affects youįeb 2010 UPDATE 1 - Special instructions for running NAST with very large RNA molecules (>1000 nucleotides) are posted on the wiki New Releases (1.0) of NAST and C2A are available! Our software package is freely available at. thermophila group I intron, creating an integrated model of the entire molecule. Finally, we used NAST to build in missing loops in the crystal structures of the Azoarcus and Twort ribozymes, and to incorporate crystallographic data into the Michel-Westhof model of the T. We successfully used ideal small-angle X-ray scattering data and both ideal and experimental solvent accessibility data to select the best cluster of structures for both tRNA and P4-P6. One advantage of NAST is the ability to rank clusters of structurally similar decoys based on their compatibility with experimental data. The coarse-grained resolution allows us to model large molecules such as the 158-residue P4-P6 or the 388-residue T. Representative structures in the best ranking clusters averaged 8.0 +/- 0.3 A and 16.3 +/- 1.0 A RMSD for the yeast phenylalanine tRNA and the P4-P6 domain of the Tetrahymena thermophila group I intron, respectively.
We demonstrate NAST's capabilities by using only secondary structure and tertiary contact predictions to generate, cluster, and rank structures. We present a protocol (the nucleic acid simulation tool ) for RNA modeling that uses an RNA-specific knowledge-based potential in a coarse-grained molecular dynamics engine to generate plausible 3D structures. However, creating three-dimensional (3D) structural models of RNA remains a significant challenge.
\).Understanding the function of complex RNA molecules depends critically on understanding their structure.
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