FR3D was developed to find small RNA motifs (two to 20 nucleotides) in RNA 3D structures from the Protein Data Bank. FR3D stands for “Find RNA 3D” and is commonly pronounced “Fred”. The main way to run motif searches is the online tool WebFR3D. With WebFR3D, one can search up to date representative sets (non-redundant lists) and the results will be accessible under stable URLs. The search engine behind WebFR3D is written in Python and is being actively improved in 2022.
The original version of FR3D is available as Matlab/Octave code. The most current version is available on the “dev” branch on Github, while the most stable version is available on the “master” branch on Github. The most current documentation of the Matlab code is toward the end of the RNA 3D structure course.
In order to carry out motif searches, we use FR3D to annotate RNA-containing 3D structure files with basepairs, stacking, and base-backbone interactions. FR3D annotations of all RNA-containing PDB files are available from the Structure Atlas at the BGSU RNA group website. The Matlab/Octave code can be used to annotate pairwise interactions as well. Python code for annotation of pairwise interactions is being developed actively in 2022.
You may also be interested in the RNA Basepair Catalog hosted at NDB and the FR3D Base-Phosphate Catalog.
Papers 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.
- WebFR3D – a server for finding, aligning and analyzing recurrent RNA 3D motifs, Anton I. Petrov; Craig L. Zirbel; Neocles B. Leontis. Nucleic Acids Research, 2011.
Requests for information and bug reports should be sent to Craig L. Zirbel via the Contact Us form.
Updated: 02/12/2022 07:32PM