ArticleNucleic acids research2011
WebFR3D--a server for finding, aligning and analyzing recurrent RNA 3D motifs.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations.Genome biology · 2025Article
- The 5'-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH.Nucleic acids research · 2024Article
- Structure of an internal loop motif with three consecutive U•U mismatches from stem-loop 1 in the 3'-UTR of the SARS-CoV-2 genomic RNA.Nucleic acids research · 2024Article
- Structural basis for cloverleaf RNA-initiated viral genome replication.Nucleic acids research · 2023Article
- Anionic G•U pairs in bacterial ribosomal rRNAs.RNA (New York, N.Y.) · 2023Article
- Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey.Molecules (Basel, Switzerland) · 2022Article
- Context-sensitivity of isosteric substitutions of non-Watson-Crick basepairs in recurrent RNA 3D motifs.Nucleic acids research · 2021Article
- Graph Theoretical Methods and Workflows for Searching and Annotation of RNA Tertiary Base Motifs and Substructures.International journal of molecular sciences · 2021Review
- Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs.PLoS computational biology · 2021Article
- Genus for biomolecules.Nucleic acids research · 2020Article
- Thermodynamic examination of pH and magnesium effect on U6 RNA internal loop.RNA (New York, N.Y.) · 2019Article
- Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families.Nucleic acids research · 2018Article
- Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction.Nucleic acids research · 2017Article
- Rational engineering of the Neurospora VS ribozyme to allow substrate recognition via different kissing-loop interactions.Nucleic acids research · 2016Article
- The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs.Methods (San Diego, Calif.) · 2016Review
- Article
- RAG-3D: a search tool for RNA 3D substructures.Nucleic acids research · 2015Article
- The NMR structure of the II-III-VI three-way junction from the Neurospora VS ribozyme reveals a critical tertiary interaction and provides new insights into the global ribozyme structure.RNA (New York, N.Y.) · 2015Article
- RNABP COGEST: a resource for investigating functional RNAs.Database : the journal of biological databases and curation · 2015Article
- Annotating RNA motifs in sequences and alignments.Nucleic acids research · 2015Article
Corrections and comments
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Authors and funding
3 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.