The database of three-dimensional interacting domains (3did) is a
biological database
Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including geno ...
containing a catalogue of
protein-protein interactions for which a high-resolution 3D structure is known.
3did collects and classifies all structural models of domain-domain interactions in the
Protein Data Bank
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which is overseen by the Worldwide Protein Data Bank (wwPDB). This structural data is obtained a ...
, providing molecular details for such interactions. 3did uses the
Pfam
Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The latest version of Pfam, 37.0, was released in June 2024 and contains 21,979 families. It is cur ...
database to define the position of
protein domains
In molecular biology, a protein domain is a region of a protein's polypeptide chain that is self-stabilizing and that folds independently from the rest. Each domain forms a compact folded three-dimensional structure. Many proteins consist of se ...
in the protein structures. 3did was first published in 2005. The current version also includes a pipeline for the discovery and annotation of novel domain-motif interactions. For every interaction 3did identifies and groups different binding modes by clustering similar interfaces into “interaction topologies”. By maintaining a constantly updated collection of domain-based structural interaction templates, 3did is a reference source of information for the structural characterization of protein interaction networks. 3did is updated every six months and is available for bulk download and for browsing at http://3did.irbbarcelona.org.
See also
*
protein interaction
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...
*
three-dimensional structures
References
External links
* http://3did.irbbarcelona.org
Protein databases
Protein structure
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