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RNA structure databases | RNA structure data analysis

RCSB PDB
Dataset

RCSB PDB The Research Collaboratory for Structural Bioinformatics Protein Data Bank

Helps students and researchers to understand all aspects of biomedicine and…

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…

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ITS2 Database
Dataset

ITS2 Database Internal Transcribed Spacer 2 Database

Provide a valid structure for every internal transcribed spacer 2 (ITS2)…

Provide a valid structure for every internal transcribed spacer 2 (ITS2) sequence. ITS2 Database contains information about the structure of more than 210 000 ITS2 molecules, nearly 80 per cent of…

NDB
Dataset

NDB Nucleic Acid Database

Performs searches based on annotations relating to sequence, structure and…

Performs searches based on annotations relating to sequence, structure and function. The Nucleic Acid Database is a web portal that provides access to information about 3D nucleic acid structures and…

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NNDB
Dataset

NNDB Nearest Neighbor DataBase

A web-based resource for disseminating parameter sets for predicting nucleic…

A web-based resource for disseminating parameter sets for predicting nucleic acid secondary structure stabilities.

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RNAJunction
Dataset

RNAJunction

Contains structure and sequence information for RNA structural elements such as…

Contains structure and sequence information for RNA structural elements such as helical junctions, internal loops, bulges and loop-loop interactions.

CCDB
Dataset

CCDB CyberCell DataBase

A comprehensive collection of detailed enzymatic, biological, chemical,…

A comprehensive collection of detailed enzymatic, biological, chemical, genetic, and molecular biological data about E. coli (strain K12, MG1655).

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RNA helicase…
Dataset

RNA helicase database

Enables to locate and retrieve comprehensive information about sequence,…

Enables to locate and retrieve comprehensive information about sequence, structure, biochemical and cellular function of RNA helicases. RNA helicase database is an online resource that provides ready…

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InterRNA
Dataset

InterRNA INTERactions in RNA structures database

Contains records of known RNA 3D motifs as well as records for clusters of…

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…

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RNA STRAND
Dataset

RNA STRAND

Contains known RNA secondary structures of any type and organism. 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…

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RNArchitecture
Dataset

RNArchitecture

Provides a comprehensive classification system that describes relationships…

Provides a comprehensive classification system that describes relationships between RNA families. RNArchitecture is an online resource that uses and organizes information from several databases…

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ITSoneDB
Dataset

ITSoneDB

Informs user about whole eukaryotic domain. ITSoneDB is a database aimed at…

Informs user about whole eukaryotic domain. ITSoneDB is a database aimed at promoting Internal Transcribed Spacer 1 (ITS1)-based metagenomic surveys. It contains more than one million ITS1 sequences…

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RNA shapes…
Desktop
Web

RNA shapes studio

A repository of components that allows us to integrate several established…

A repository of components that allows us to integrate several established tools for RNA structure analysis: RNAshapes, RNAalishapes and pknotsRG, including its recent extension pKiss.

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Structure…
Dataset

Structure Surfer

A database and visualization tool for inspecting RNA secondary structure in six…

A database and visualization tool for inspecting RNA secondary structure in six transcriptome-wide data sets from human and mouse. The data sets were generated using four different high-throughput…

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Voronoia4RNA
Dataset

Voronoia4RNA

A database storing data on atomic packing densities of RNA structures and…

A database storing data on atomic packing densities of RNA structures and complexes. Compared to other methods, that solely estimate van der Waals interactions i.e. by gain of solvent excluded…

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RNA CoSSMos
Dataset
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BPS
Dataset

BPS

A database of RNA base pairs with quantitative information on the spatial…

A database of RNA base pairs with quantitative information on the spatial arrangements of interacting bases, including higher-order base associations, and the context of these interactions in…

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URSDB
Dataset

URSDB Universe of RNA Structures DataBase

A database that stores information obtained from all RNA-containing PDB…

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…

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MPGAfold
Desktop

MPGAfold Massively Parallel Genetic Algorithm

A genetic algorithm to explore the very large search space of RNA secondary…

A genetic algorithm to explore the very large search space of RNA secondary structure conformations for an optimal solution. MPGAfold operates on a population of thousands of possible solution…

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Mc-Annotate
Desktop
Web

Mc-Annotate

Extracts and manipulates structural information, to simplify further structural…

Extracts and manipulates structural information, to simplify further structural analyses and searches, and to objectively represent structural knowledge. Mc-Annotate allows one to classify the…

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UNITE
Dataset

UNITE

Provides a database for high-quality reference records of internal transcribed…

Provides a database for high-quality reference records of internal transcribed spacer (ITS) sequences. UNITE is an online resource that targets all fungi and geographical regions, to provide reliable…

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HD-RNAS
Dataset

HD-RNAS Hierarchical Database of RNA Structures

Provides a classification of functional RNA structures available in Protein…

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…

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RKB
Desktop

RKB RNA Knowledge Base

Captures structure-based knowledge about ribonucleic acids (RNA) using RDF/OWL…

Captures structure-based knowledge about ribonucleic acids (RNA) using RDF/OWL Semantic Web technologies. RKB consists of an RNA Ontology with basic terminology for nucleic acid composition along…

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RNABase
Dataset

RNABase

Hosts all three-dimensional structures containing RNA deposited in either the…

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…

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