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.
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 their complexes. It contains derived geometric data, classifications of structures and motifs, standards for describing nucleic acid features, as well as tools and software for the analysis of nucleic acids.
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 all ITS2 sequences in GenBank, covering all major taxonomic units. The platform equally offers tools that can automatically align calculation as well as build tree reconstruction considering both, sequences AND secondary structures.
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 reference sequences for molecular identification. To generate a concise set of reference sequences, it applies a two-tier clustering process, first clustering all sequences to approximately the subgenus/genus level and then applies it to the species level.
Generates functional genomic data in brain samples. The CMC data brain was obtained from autopsies of cases with and without severe psychiatric disorders. This database includes over 1,150 samples and represents one of the biggest collection of collaborating brain banks. These samples generates a wide spectrum of data comprising regional gene expression, epigenomics, whole genome sequencing (WGS), and somatic mosaicism.
A database containing structural, functional and sequence data related to RNA pseudo-knots. For each pseudoknot, thirteen items are stored, for example the relevant sequence, the stem positions of the pseudoknot, the EMBL accession number of the sequence and the support that can be given regarding the reliability of the pseudo-knot.
Provides a RNA mapping repository. RMDB allows users to deposit and search curated structure mapping measurements in both human- and machine-readable formats. The database offers (i) browsing each entry using the data visualization tools, (ii) comparisons of mapping data against structural models, (iii) downloading data in either RDAT or SNRNASM format or direct export, and (iv) a secondary structure prediction server.
Provides a resource for the automatic search of user tailored, three dimensional fragments within a set of RNA structures. RNA FRABASE is a web-accessible database with an engine for automatic search of the 3D fragments. It includes a large collection of structural data about RNA molecules, in both their isolated and complexed form, all of which is derived from their PDB deposited atom coordinates.
Stores information about recurrent RNA 3D motifs and their interactions, found in experimentally determined RNA structures and in RNA-protein complexes. Besides, the search utility enables searching 'RNA bricks' according to sequence similarity, and makes it possible to identify motifs with modified ribonucleotide residues at specific positions.
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.
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.
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 access to sequence, structure, biochemical and cellular function of all RNA helicases from the most widely used model organisms. This database also emphasizes phylogenetic relations between related RNA helicases.
Gathers and classifies all possible RNA 2D topologies, including existing and hypothetical motifs. RAG offers a graphical representation of RNA secondary structure using elements of graph theory, including tree and dual graphs, adjacency matrices, and Laplacian eigenvalues. It can be used for prediction of non-coding RNAs, modification of RNA graph representations into labeled and directed graphs, and RNA structural analysis.
Provides a comprehensive classification system that describes relationships between RNA families. RNArchitecture is an online resource that uses and organizes information from several databases (Rfam, Protein Data Bank). This database contains more than 2600 families and can also serves as a repository of theoretical models of RNA 3D structures.
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 spanning over 134 000 species. Single or multiple entries can be selected for web visualization and/or retrieval through different query options. User can browse this platform by three ways: thanks to a simple search, a tree search, and an advanced search.
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.