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RNA structure databases

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RCSB PDB / The Research Collaboratory for Structural Bioinformatics Protein Data Bank
Helps students and researchers to understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. RCSB PDB is a database that provides a resource powered by the Protein Data Bank (PDB) archive - information about the 3D shapes of proteins, nucleic acids, and complex assemblies. Users can perform simple and complex queries on the data, analyze, and visualize the results.
RNA Base Triples Database
Hosts observed and modeled base triples, organized in two ways, by geometric triple family and by three-base combination. The RNA Base Triples Database provides separate web pages for each base triple family and for each three-base combination. To view a particular base triple family, the user clicks on the cell corresponding to that family. In this table, green colored cells indicate families with observed instances of fully annotated base triples. The number in each cell reports the number of distinct base combinations observed for that family. Yellow cells designate families having no fully annotated instances. The classification helps to identify recurrent triple motifs that can substitute for each other while conserving RNA 3D structure, with applications in RNA 3D structure prediction and analysis of RNA sequence evolution.
CompaRNA
Provides an automated system for the continuous evaluation of RNA structure prediction methods. The goal of CompaRNA is to provide a ‘blind’ benchmark using experimental data before it becomes incorporated in the training data set of the assessed prediction methods. In analogy to protein structure prediction benchmarks Livebench and EVA, CompaRNA uses as a reference experimentally solved RNA structures deposited in the Protein Data Bank (PDB). It also provides the community with a ‘static’ benchmark, generated on a data set extracted from the RNAstrand database, which contains experimentally verified RNA secondary structures of any type and organism. RNAstrand includes a larger number of molecules than those with solved 3D structures, and it covers sequences that are on the average longer than those with known 3D structures. These benchmarks offer insight into the relative performance of different RNA secondary structure prediction methods on different types of RNA sequences and structures.
InterRNA / INTERactions in RNA structures database
Contains records of known RNA 3D motifs as well as records for clusters of bases that are interconnected by hydrogen bonds. The contents of the database were compiled from RNA structural annotations carried out by the NASSAM and COGNAC computer programs. Users have the choice of three searching methods: (i) an option to select a pre-determined set of arrangements and motifs; (ii) an option to search for base interaction annotations in a specific PDB structure using a PDB ID query or by using the unique database identifier; and (iii) a keyword search option. An analysis of the database content and comparisons with the existing corpus of knowledge regarding RNA 3D motifs clearly show that InterRNA is able to provide an extension of the annotations for known motifs as well as able to provide novel interactions for further investigations.
FoldAtlas
Provides convenient access to in vivo RNA structure probing data across thousands of transcripts. FoldAtlas allows a researcher to easily locate, view, and retrieve probing data for a given RNA molecule. FoldAtlas also provides in silico and in vivo secondary structure predictions for comparison, visualised in the browser as circle plots and topology diagrams. Datasets included are from a new high-depth Structure-seq DMS analysis in Arabidopsis thaliana, covering over 11,000 transcripts.
RNA 3D Motif Atlas
Offers an automated pipeline based on a comprehensive framework for extracting, analyzing, and classifying RNA 3D motifs. RNA 3D motif atlas is a comprehensive and representative collection of internal and hairpin loop RNA 3D motifs extracted from the representative sets of RNA 3D structures. All data are presented in a fully transparent and coherent way in the online resource, which is both the final product of the project and the tool for understanding and improving the motif classification and analysis.
HD-RNAS / Hierarchical Database of RNA Structures
Provides a classification of functional RNA structures available in Protein Data Bank (PDB). HD-RNAS classified RNA structures in 9 major functional classes. Each class is further classified according to the source organism from which the RNA molecules were isolated and crystallized. HD-RNAS contains 1060 crystal structures, containing 3066 RNA chains. The proper source organisms of 62 RNA structures have been revealed by BLAST search that were designated as synthetic in the PDB entries. The non-redundant set of structures consists of 376 PDB entries, indicating the best representative structures from each of the sub-classes based on their resolution and R-factor.
Ring Catalog
An in silico solution to this design problem by combinatorial assembly of RNA 3-way junctions, bulges, and kissing loops, and tabulating the cases that lead to ring formation. The identified ring structures have been made available in Ring Catalog. As an example of a potential use of this resource, we chose a predicted RNA square structure consisting of five RNA strands and demonstrate experimentally that the self-assembly of those five strands leads to the formation of a square-like complex.
RNA STRAND
Contains known RNA secondary structures of any type and organism. RNA STRAND provides access to detailed information on known secondary structures as well as statistical analyses of structural aspects of various types of RNAs. The database provides a convenient web interface to its major functions and supports searches according to many criteria, including properties of secondary structure elements. RNA STRAND is publicly accessible and supports the submission of new RNA structures by the research community.
RNABP COGEST / RNA Base Pair Count, Geometry and Stability
Brings together information, extracted from literature data, regarding occurrence frequency, experimental and quantum chemically optimized geometries, and computed interaction energies, for non-canonical base pairs observed in a non-redundant dataset of functional RNA structures. RNABP COGEST is designed to enable the quantum mechanical (QM) community, on the one hand, to identify appropriate biologically relevant model systems and also enable the biology community to easily sift through diverse computational results to gain theoretical insights which could promote hypothesis driven biological research.
URSDB / Universe of RNA Structures DataBase
A database that stores information obtained from all RNA-containing PDB entries. URSDB consists of 51 tables containing indexed data on various elements of the RNA structures. The database provides a web interface allowing user to select a subset of structures with desired features and to obtain various statistical data for a selected subset of structures or for all structures. In particular, one can easily obtain statistics on geometric parameters of base pairs, on structural motifs (stems, loops, etc.) or on different types of pseudoknots.
SCOR / Structural Classification Of RNA
Obsolete
Provides a comprehensive perspective and understanding of RNA motif three-dimensional structure, function, tertiary interactions and their relationships. The web interface provides a straightforward but flexible means to explore the multi‐layered classification of SCOR. Users are given a standard set of icons and buttons to navigate the classes. The interface allows the user to view multiple parallel classes, subclasses (i.e. child classes) and paths simultaneously. The user may also choose to focus on a single class or path along a branch of the hierarchy—or may choose a combination of views.
RNABase
Obsolete
Hosts all three-dimensional structures containing RNA deposited in either the Protein Data Bank (PDB) or Nucleic Acid Data Base (NDB). For each structure, RNABase contains a brief summary as well as annotation of conformational parameters, identification of possible model errors, Ramachandran-style conformational maps and classification of ribonucleotides into conformers. These same analyses can also be performed on structures submitted by users. To facilitate access, structures are automatically placed into a variety of functional and structural categories, including: ribozymes, pseudoknots, etc.
HyPaLib / Hybrid Pattern Library
Obsolete
Gathers information and annotated structural elements characteristic for certain classes of structural and functional RNAs. HyPaLib is an online repository containing sequential and structural elements characteristic for different classes of RNA. It offers several types of entries such as: (1) simple patterns of DNA or RNA sequences; (2) simple patterns of RNA secondary structure; (3) patterns for RNA protein binding motifs; (4) patterns describing chemically and catalytically active motifs; or (5) patterns describing small molecule-binding RNA motifs.
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