ArticleNucleic acids research2012
RNA CoSSMos: Characterization of Secondary Structure Motifs--a searchable database of secondary structure motifs in RNA three-dimensional structures.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
29 citing papers in PubMed.
- A large-scale cryo-EM RNA motif dataset and benchmark for machine learning-based structure modeling.Computational biology and chemistry · 2026Article
- A Large-Scale Cryo-EM RNA Motif Dataset and Benchmark for Machine Learning-Based Structure Modeling.bioRxiv : the preprint server for biology · 2026Article
- A workflow to define structural classes and classify nucleic acids circular dichroism spectra.QRB discovery · 2025Review
- Prediction of 3D RNA Structures from Sequence Using Energy Landscapes of RNA Dimers: Application to RNA Tetraloops.Journal of chemical theory and computation · 2024Article
- Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation.Nature communications · 2024Article
- Conformational dynamics of RNA G4C2 and G2C4 repeat expansions causing ALS/FTD using NMR and molecular dynamics studies.Nucleic acids research · 2023Article
- Crystal structure of a highly conserved enteroviral 5' cloverleaf RNA replication element.Nature communications · 2023Article
- Identification and characterization of RNA pentaloop sequence families.NAR genomics and bioinformatics · 2023Article
- Evaluating Geometric Definitions of Stacking for RNA Dinucleoside Monophosphates Using Molecular Mechanics Calculations.Journal of chemical theory and computation · 2022Article
- RNA CoSSMos 2.0: an improved searchable database of secondary structure motifs in RNA three-dimensional structures.Database : the journal of biological databases and curation · 2020Article
- Identification and Characterization of New RNA Tetraloop Sequence Families.Biochemistry · 2019Article
- bpRNA: large-scale automated annotation and analysis of RNA secondary structure.Nucleic acids research · 2018Article
- Sequence-Based Prediction of RNA-Binding Residues in Proteins.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Bioinformatics Study of Structural Patterns in Plant MicroRNA Precursors.BioMed research international · 2017Article
- Computational Generation of RNA Nanorings.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Cellular Delivery of RNA Nanoparticles.ACS combinatorial science · 2016Review
- URS DataBase: universe of RNA structures and their motifs.Database : the journal of biological databases and curation · 2016Article
- Computational investigation of RNA CUG repeats responsible for myotonic dystrophy 1.Journal of chemical theory and computation · 2015Article
- RNABP COGEST: a resource for investigating functional RNAs.Database : the journal of biological databases and curation · 2015Article
- RNA Bricks--a database of RNA 3D motifs and their interactions.Nucleic acids research · 2014Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
RNA secondary structure is important for designing therapeutics, understanding protein-RNA binding and predicting tertiary structure of RNA. Several databases and downloadable programs exist that specialize in the three-dimensional (3D) structure of RNA, but none focus specifically on secondary structural motifs such as internal, bulge and hairpin loops. The RNA Characterization of Secondary Structure Motifs (RNA CoSSMos) database is a freely accessible and searchable online database and website of 3D characteristics of secondary structure motifs. To create the RNA CoSSMos database, 2156 Protein Data Bank (PDB) files were searched for internal, bulge and hairpin loops, and each loop's structural information, including sugar pucker, glycosidic linkage, hydrogen bonding patterns and stacking interactions, was included in the database. False positives were defined, identified and reclassified or omitted from the database to ensure the most accurate results possible. Users can search via general PDB information, experimental parameters, sequence and specific motif and by specific structural parameters in the subquery page after the initial search. Returned results for each search can be viewed individually or a complete set can be downloaded into a spreadsheet to allow for easy comparison. The RNA CoSSMos database is automatically updated weekly and is available at http://cossmos.slu.edu.
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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.