WebFR3D

WebFR3D is the online version of FR3D, a suite of Matlab 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.

Geometric Search

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.

Launch a geometric search

Symbolic Search

Use symbolic search to look for an arbitrary RNA fragment. The user can specify nucleotide identities, interactions between nucleotides and distances in the polyribonucleotide strand.  This can be used to search for arbitrary sets of nucleotides making certain types of interactions. This includes searching for RNA motifs, base pairs, base triples, kissing loops, loop-receptor interactions etc.  It can also be used to check if an internal or hairpin loop seen in a secondary structure is present in 3D structures.

Launch a symbolic search

 

WebFR3D is described in:

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.

The original publication about FR3D:

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 Biology56, 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.