FR3D stands for “Find RNA 3D” and is commonly pronounced “Fred”. It was developed to find small RNA motifs (two to 20 nucleotides) in PDB files. It is available as Matlab/Octave code that has been tested on the PC, Macintosh, and UNIX. The most current version is available on the “dev” branch on Github at this link, while the most stable version is available on the “master” branch on Github at this link. The most current documentation is toward the end of the RNA 3D structure course materials at this link. WebFR3D, the online version of FR3D, is also available. There, one can search up to date non-redundant lists and the results will be accessible under stable URLs. FR3D annotations of all RNA-containing PDB files are available by from BGSU at this link or from NDB at this link by looking up the structure of interest. You may also be interested in the RNA Basepair Catalog hosted at NDB and the FR3D Base-Phosphate Catalog

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References in zbMATH (referenced in 5 articles )

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  1. Rahrig, Ryan R.: A new method for RNA 3d structural comparisons using simulated annealing (2015)
  2. Lamiable, Alexis; Barth, Dominique; Denise, Alain; Quessette, Franck; Vial, Sandrine; Westhof, Éric: Automated prediction of three-way junction topological families in RNA secondary structures (2012)
  3. Ciriello, Giovanni; Gallina, Claudio; Guerra, Concettina: Analysis of interactions between ribosomal proteins and RNA structural motifs (2010) ioport
  4. Kirillova, Svetlana; Tosatto, Silvio C. E.; Carugo, Oliviero: FRASS: the web-server for RNA structural comparison (2010) ioport
  5. Sarver, Michael; Zirbel, Craig L.; Stombaugh, Jesse; Mokdad, Ali; Leontis, Neocles B.: FR3D: Finding local and composite recurrent structural motifs in RNA 3D structures (2008)