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
- Redesigned 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, firstname.lastname@example.org
- Documentation on new search input page is very thin; consult the examples.
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.
Older, Matlab-based WebFR3D described below
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.
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.
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 origional 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.