We recently 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, 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.
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.