Data collections tagging

Here are the data collections associated to the following tag:

  • domain (A domain is a protein subsequence that forms a three-dimensional structure, and can provide specific catalytic or binding sites as found in enzymes or regulatory proteins. A specific domain may appear in a variety of evolutionarily related proteins.)
NameDefinition
BYKdb The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information.
CAPS-DB CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps.
Conserved Domain Database The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution.
Cube db Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available.
CutDB The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites).
ELM Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances.
Homeodomain Research The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders.
InterPro InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.
Molecular Modeling Database The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites.
Pfam The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored.
ProDom ProDom is a database of protein domain families generated from the global comparison of all available protein sequences.
PROSITE PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.
RFAM The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion.
ScerTF ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor.
SitEx SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments.
SMART The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures.
SPRINT SPRINT provides search access to the data bank of protein family fingerprints (PRINTS).
SubstrateDB The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates.
TopFind TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.

19 items returned.