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.
Use geometric search to find other instances of a given RNA fragment. Required input: PDB id, nucleotide numbers.
- Search for RNA 3D motifs, such as sarcin, kink-turn, C-loop, GNRA tetraloop, T-loop and others.
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.
- 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.
- Check if an internal or hairpin loop seen in a secondary structure is present in 3D structures.
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 Biology. 56, Nos. 1-2, January 2008.