Rosetta FARFAR (RNA De Novo) Protocol

[Submit FARFAR task]

[FARFAR Queue]

[FARFAR Documentation]

Please cite the following article when referring to results from our ROSIE server:

  1. Das, R., Karanicolas, J., and Baker, D. (2010), "Atomic accuracy in predicting and designing noncanonical RNA structure". Nature Methods 7:291-294. Link [This is the primary citation for these algorithms]
  2. Lyskov S, Chou FC, Conchúir SÓ, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, Gray JJ, Das R., "Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)". PLoS One. 2013 May 22;8(5):e63906. doi: 10.1371/journal.pone.0063906. Print 2013. Link

Additional references of interest:

  • Sripakdeevong, P., Kladwang, W., and Das, R. (2011) "An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling", PNAS 108:20573-20578. Link [a new way to solve RNA models, available in the Rosetta codebase]
  • Kladwang, W., VanLang, C.C., Cordero P., and Das, R. (2011) "A two-dimensional mutate-and-map strategy for non-coding RNA structure", Nature Chemistry 3: 954-962. Link [Presents method for assembling larger RNA structures with high-throughput experimental constraints]
  • Das, R. and Baker, D. (2007), "Automated de novo prediction of native-like RNA tertiary structures", PNAS 104: 14664-14669. Link [for fragment assembly witout full atom refinement]
  • Sripakdeevong, P., Cevec, M., Chang, A.T., Erat, M.C., Ziegeler, M., Zhao, Q., Fox, G.E., Gao, X., Kennedy, S.D., Kierzek, R., Nikonowicz, E.P., Schwalbe, H., Sigel, R.K.O., Turner, D.H. and Das, R. (2012) “Consistent structure determination of noncanonical RNA motifs from 1H NMR chemical shift data”, in revision. Link [ROSETTA RNA denovo modeling with 1H NMR chemical shift data]

RNA modeling tools developed by the Das lab at Stanford