FR3D

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 was re-written in Python in 2022.  WebFR3D was re-deployed as a Python Flask application on our new server in September 2024.

In order to carry out motif searches, we use FR3D to annotate RNA-containing 3D structure files with basepairs, stacking, base-backbone interactions, and more.  FR3D annotations of all RNA-containing PDB files are available from the Structure Atlas at the BGSU RNA group website. 

The best version of FR3D for local use is written in Python.  See the fr3d-python repository on GitHub.  The "master" branch is the most stable, while the "latest" branch is the most current.

The original version of FR3D is available as Matlab/Octave code, but it has not been updated for some years.  The most current documentation of the Matlab code is toward the end of the RNA 3D structure course. The most current Matlab version is available on the “dev” branch on Github, while the most stable version is available on the “master” branch on Github. The Matlab code can be used to annotate pairwise interactions and to carry out motif searches.

You may also be interested in the RNA Basepair Catalog hosted at NDB and the RNA Base-Phosphate Catalog.

Papers to cite:

Requests for information and bug reports should be sent to Craig L. Zirbel via the Contact Us form.

Updated: 10/04/2024 04:18PM