Understanding the function of complex RNA molecules depends critically on understanding their structure. However, creating three-dimensional (3D) structural models of RNA remains a significant challenge. We present a protocol (the nucleic acid simulation tool [NAST]) for RNA modeling that uses an RNA-specific knowledge-based potential in a coarse-grained molecular dynamics engine to generate plausible 3D structures. We demonstrate NAST's capabilities by using only secondary structure and tertiary contact predictions to generate, cluster, and rank structures. 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. The coarse-grained resolution allows us to model large molecules such as the 158-residue P4-P6 or the 388-residue T. thermophila group I intron. One advantage of NAST is the ability to rank clusters of structurally similar decoys based on their compatibility with experimental data. 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. 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. thermophila group I intron, creating an integrated model of the entire molecule. Our software package is freely available at https://simtk.org/home/nast.
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NAST permits experimentalists to use coarse grained molecular dynamics and a knowledge-based force field to generate RNA structures that are consistent with experimentally determined structural data.
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August 2010 UPDATE
New Releases (1.0) of NAST and C2A are available!
Lots of exciting new features, detailed in the new manual NastTutorial.v4.pdf (under the "Downloads" button on the left).
C2A has been separated from NAST, please download and install separately from the C2A project page: simtk.org/home/c2a.
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Feb 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 you
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Feb 2010 UPDATE 1 - Special instructions for running NAST with very large RNA molecules (>1000 nucleotides) are posted on the wiki
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Nov 09 UPDATE - NAST is now available on most unix/pc/mac platforms. Please read the instructions posted on the wiki for details.
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NAST (Nucleic Acid Simulation Toolkit) is a knowledge-based coarse-grained tool for modeling RNA structures. It produces a diverse set of plausible 3D structures that satisfy user-provided constraints based on:
1. primary sequence
2. known or predicted secondary structure
3. known or predicted tertiary contacts (optional)
Additionally, NAST can use residue-resolution experimental data (e.g. hydroxyl radical footprinting) to filter the generated decoy structures.
NAST uses an RNA-specific knowledge-based potential in a coarse-grained molecular dynamics engine to generate large numbers of plausible 3D structures that satisfy the constraints given on the secondary and tertiary structure. It then filter these structures based on agreement to the experimental data (if available). This results in a model of the molecule which satisfies all the known residue-resolution data.
TO USE NAST: Please read the README file under the downloads section.
News
Bug fix for C2A end pieces of length 1
Feb 18, 2010If 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 you.
Running NAST with very large RNA molecules
Feb 18, 2010Special instructions for running NAST with very large RNA molecules (>1000 nucleotides) are posted on the wiki.
NAST now runs on 64bit Unix and Mac OSX Snow Leopard.
Nov 3, 2009You can now build and install NAST on 64bit unix machines and Mac OSX machines running snow leopard.
NAST and C2A tools now available for 3D RNA modeling
Jun 10, 2009The Nucleic Acid Simulation Tool (NAST) and its related tool, Coarse to Atomic (C2A), have just been released.
Downloads
NAST package for modeling coarse grain structures from primary, secondary and tertiary structure data. Includes examples from Jonikas at al. 2009.
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