Paper Info
Title
WebFR3D - a server for finding, aligning and analyzing recurrent RNA 3D motifs.
Abstract
WebFR3D is the on-line version of 'Find RNA 3D' (FR3D), a program for annotating atomic-resolution RNA 3D structure files and searching them efficiently to locate and compare RNA 3D structural motifs. WebFR3D provides on-line access to the central features of FR3D, including geometric and symbolic search modes, without need for installing programs or downloading and maintaining 3D structure data locally. In geometric search mode, WebFR3D finds all motifs similar to a user-specified query structure. In symbolic search mode, WebFR3D finds all sets of nucleotides making user-specified interactions. In both modes, users can specify sequence, sequence-continuity, base pairing, base-stacking and other constraints on nucleotides and their interactions. WebFR3D can be used to locate hairpin, internal or junction loops, list all base pairs or other interactions, or find instances of recurrent RNA 3D motifs (such as sarcin-ricin and kink-turn internal loops or T- and GNRA hairpin loops) in any PDB file or across a whole set of 3D structure files. The output page provides facilities for comparing the instances returned by the search by superposition of the 3D structures and the alignment of their sequences annotated with pairwise interactions. WebFR3D is available at http://rna.bgsu.edu/webfr3d.
Year
DOI
Venue
2011
10.1093/nar/gkr249
NUCLEIC ACIDS RESEARCH
Keywords
Field
DocType
server,nucleotides,internet,rna
Pairwise comparison,RNA,Biology,Upload,Theoretical computer science,Software,Structural motif,Bioinformatics,Genetics,Base pair,Protein Data Bank (RCSB PDB)
Journal
Volume
Issue
ISSN
39
SUPnan
0305-1048
Citations 
PageRank 
References 
9
0.63
11
Authors
3
Name
Order
Citations
PageRank
Anton I Petrov1444.40
Craig L Zirbel2604.96
Neocles B Leontis3916.13