Tools for the automatic identification and classification of RNA base pairs

  title={Tools for the automatic identification and classification of RNA base pairs},
  author={Huanwang Yang and Fabrice Jossinet and Neocles B. Leontis and Li Chen and John D. Westbrook and Helen M. Berman and Eric Westhof},
  journal={Nucleic acids research},
  volume={31 13},
Three programs have been developed to aid in the classification and visualization of RNA structure. BPViewer provides a web interface for displaying three-dimensional (3D) coordinates of individual base pairs or base pair collections. A web server, RNAview, automatically identifies and classifies the types of base pairs that are formed in nucleic acid structures by various combinations of the three edges, Watson-Crick, Hoogsteen and the Sugar edge. RNAView produces two-dimensional (2D) diagrams… 
DSSR: an integrated software tool for dissecting the spatial structure of RNA
A new, inclusive definition of DSSR (Dissecting the Spatial Structure of RNA), an integrated and automated tool for analyzing and annotating RNA tertiary structures, provides a novel perspective on the spatial organization of RNA.
BPS: a database of RNA base-pair structures
The BPS is a database of RNA base-pair structures, higher-order base interactions and isosteric pairs (base pairs with similar shape) to find and annotate the structural and chemical features of the Watson-Crick and non-Watson–Crick base pairs in high-resolution RNA structures, and to provide a user-friendly interface to browse and search for the base pairs.
RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures
The RNA FRABASE is a web-accessible engine with a relational database, which allows for the automatic search of user-defined, 3D RNA fragments within a set of RNA structures. This is a new tool to
FR3D: finding local and composite recurrent structural motifs in RNA 3D structures
It is demonstrated that FR3D finds all occurrences, both local and composite and with nucleotide substitutions, of sarcin/ricin and kink-turn motifs in the 23S and 5S ribosomal RNA 3D structures of the H. marismortui 50S ribOSomal subunit and assigns the lowest discrepancy scores to bona fide examples of these motifs.
Computational Approaches for Investigating Three-Dimensional Structures of RNA
Approach which use graph theory have proven to be effective when employed for automatic identification of interaction patterns and structural motifs present in RNA tertiary structures and the comparison of RNA folds and the prediction of novel folds.
jVIz.Rna - A tool for visual comparison and analysis of RNA secondary structures
JViz.Rna is a tool designed to assist in the analysis of structure predictions with three unique features: analysis of multiple structures using seven different visualization methods, dual graphs of RNA structures which highlight the topology of the RNA, and the ability to overlay a predicted structure on top of the native structure of a given RNA in all visualizations apart from dual graphs which use a different comparison method.
Automated extraction and classification of RNA tertiary structure cyclic motifs
A minimum cycle basis of the tertiary structure of a large ribosomal subunit (LSU) X-ray crystal structure was analyzed and the cycles identified correspond to small and cyclic motifs that compose most of the LSU RNA tertiaries structure and contribute to its thermodynamic stability.
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
While RNA secondary structure prediction from sequence data has made remarkable progress, there is a need for improved strategies for annotating the features of RNA secondary structures. Here we
The ARTS web server for aligning RNA tertiary structures
A web server built around ARTS, a method for aligning tertiary structures of nucleic acids (both RNA and DNA), which has been used to conduct an all-against-all comparison of all the RNA structures in the Protein Data Bank.


Quantitative analysis of nucleic acid three-dimensional structures.
A new computer program to annotate DNA and RNA three-dimensional structures, MC-Annotate, is introduced, which was used to build databases of nucleotide conformations and base-base interactions and to identify irregular regions and possible stereochemical errors in 3-D structures without interactive visualization.
Geometric nomenclature and classification of RNA base pairs.
This work proposes a classification based on the observation that the planar edge-to-edge, hydrogen-bonding interactions between RNA bases involve one of three distinct edges: the Watson-Crick edge, the Hoogsteen edge, and the Sugar edge, which facilitates the recognition of recurrent three-dimensional motifs from comparison of homologous sequences.
Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules
Using a modular sequence-analysis approach, recurrent motifs related to the sarcin–ricin loop of 23S RNA and to loop E from 5S RNA were predicted in universally conserved regions of the large ribosomal RNAs before the publication of high-resolution, atomic-level structures of representative examples of 16S and 23S rRNA molecules in their native contexts.
RNA canonical and non-canonical base pairing types: a recognition method and complete repertoire.
The problem of systematic and objective identification of canonical and non-canonical base pairs in RNA three-dimensional (3D) structures was studied, and an algorithm and its implementation in a computer program that detects and analyzes all the base pairs contained in RNA 3D structures were developed.
The non-Watson-Crick base pairs and their associated isostericity matrices.
This paper presents the 4 x 4 'isostericity matrices' summarizing the geometric relationships between the 16 pairwise combinations of the four standard bases, A, C, G and U, and helps identify isosteric pairs that co-vary or interchange in sequences of homologous molecules while maintaining conserved three-dimensional motifs.
RNAML: a standard syntax for exchanging RNA information.
This RNAML syntax allows for the storage and the exchange of information about RNA sequence and secondary and tertiary structures and permits the description of higher level information about the data including, but not restricted to, base pairs, base triples, and pseudoknots.
The kink‐turn: a new RNA secondary structure motif
A derived consensus secondary structure for the K‐turn includes 10 consensus nucleotides out of 15, and predicts its presence in the 5′‐UTR of L10 mRNA, helix 78 in Escherichia coli 23S rRNA and human RNase MRP.
Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution.
  • M. Lu, T. Steitz
  • Biology, Chemistry
    Proceedings of the National Academy of Sciences of the United States of America
  • 2000
The crystal structure of Escherichia coli ribosomal protein L25 bound to an 18-base pair portion of 5S ribosomal RNA, which contains "loop E," has been determined at 1.8-A resolution. The protein
Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle.
Analysis of the crystal structure of the universally conserved RNA-protein core of the Escherichia coli SRP revealed minor groove recognition of the 4.5 S RNA component by the M domain of the Ffh protein.
Metal ions and flexibility in a viral RNA pseudoknot at atomic resolution
The structures of two crystal forms of the frameshifting RNA pseudoknot from beet western yellow virus offer the most detailed view yet of the conformational preference and flexibility of an RNA Pseudoknot.