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 in two forms, as Matlab code that has been tested on the PC, Macintosh, and UNIX, and as a PC executable version that does not require a Matlab license. WebFR3D, the online version of FR3D, is also available. FR3D annotations of all PDB files are available at the RNA 3D Hub. FR3D also powers R3D Align, a web application for RNA 3D structural alignment. You may also be interested in the FR3D Basepair Catalog and FR3D Base-Phosphate Catalog.

The old FR3D website is available here.

Download FR3D from GitHub  Try WebFR3D


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 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.