WebFR3D

The BGSU RNA website moved to a new server on September 10, 2024.  WebFR3D is re-deployed as of September 26.  It seems to be working well.  You can try WebFR3D here and we will be happy to have your feedback. The URLs of previously-generated queries should work fairly well.  New features in Fall 2024:

• Search for modified RNA nucleotides by entering "RNA modified" in the diagonal boxes
• Basepairs and other pairwise interactions made by modified nucleotides are annotated and searchable
• Oxygen stacking interactions are available; use "sO" in the yellow boxes to get started

WebFR3D is the online version of FR3D, a suite of programs designed to search RNA 3D structures for user specified queries. To find out more about WebFR3D, take a look at the tutorial and help pages, plus a YouTube playlist of video tutorials.

We deployed a new WebFR3D search engine, written in Python by William Xi, in August 2019.  Advantages:

• Searches run more quickly
• Possible to search current representative sets and recently-released structures
• Improved input and output pages
• Output page shows results as they accumulate
• Queries can be re-loaded, modified, and launched again

• User may not be informed when the program crashes; if no results appear after 10 minutes, it probably crashed.  Check your query, then write to Craig Zirbel, zirbel@bgsu.edu

Use geometric search to find other instances of a given RNA fragment. Required input: PDB id, nucleotide numbers.  This can be used to search for RNA 3D motifs, such as sarcin, kink-turn, C-loop, GNRA tetraloop, T-loop and others.  You can constrain the instances to have various symbolic relations between nucleotides.  You can use just symbolic constraints to find instances of a motif without starting from a known fragment.

Launch a WebFR3D Search

WebFR3D is described in these articles:

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.

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. 56, Nos. 1-2, January 2008.

WebFR3D is developed and maintained by the RNA bioinformatics group at Bowling Green State University. This work is supported by grants from NIH and NSF.