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.
Paper to cite: FR3D: Finding Local and Composite Recurrent Structural Motifs in RNA 3D Structures, Michael Sarver; Craig L. Zirbel; Jesse Stombaugh; Ali Mokdad; Neocles B. Leontis. Journal of Mathematical Biology (2008) 56:215–252. Article in pdf format
The very old FR3D website is available here.
The User’s manual describes how to install the Matlab code and the PC executable version, how to start FR3D, and how to conduct searches. In order to run the PC executable version, you will need the Matlab MCR installer (150 MB).
Additional documentation describes each Matlab program in FR3D and displays the dependency between them. Matlab users can run additional programs to analyze basepairs.
PDB files are available at the RCSB Protein Data Bank.
Requests for information and bug reports should be sent to Craig L. Zirbel via the Contact Us form.