Fragment Assembly of RNA with Full Atom Refinement (FARFAR) is a framework within the Rosetta suite that can produce de novo or homologous RNA structure models and has been improved with the release of FARFAR 2, enabling larger target RNAs to be modeled 1,2. The target RNA sequence and predicted secondary structure or known homologies are utilized as inputs prior to fragment assembly. Constructs that pass quality control filters are then subjected to full atom refinement prior to producing clustered ensembles. Additional information on FARFAR 2 can be found at:
 Das, R., Karanicolas, J., and Baker, D. (2010), "Atomic accuracy in predicting and designing noncanonical RNA structure". Nature Methods 7:291-294.
 Watkins, A. M.; Rangan, R.; Das, R. “FARFAR2: Improved de novo Rosetta prediction of complex global RNA folds.” Structure, 2020, 28: 963-976.