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.
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Jonikas MA, Radmer RJ, Laederach A, Das R, Pearlman S, Herschlag D, Altman RB.
Coarse-grained modeling of large RNA molecules with knowledge-based potentialsand structural filters.
RNA. 2009 Feb;15(2):189-99.PMID: 19144906 (2009)