3did

The database of three-dimensional interacting domains (3did) is a biological database containing a catalogue of protein-protein interactions for which a high-resolution 3D structure is known.[1] 3did collects and classifies all structural models of domain-domain interactions in the Protein Data Bank, providing molecular details for such interactions. 3did uses the Pfam database to define the position of protein domains in the protein structures. 3did was first published in 2005.[2] 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.[3]

3did
Content
Descriptionidentification and classification of domain-based interactions of known three-dimensional structure.
Contact
LaboratoryInstitute for Research in Biomedicine, Barcelona, Spain.
AuthorsAmelie Stein
Primary citationStein & al. (2011)[1]
Release date2010
Access
Websitehttp://3did.irbbarcelona.org

See also

References
  1. Stein, Amelie; Céol Arnaud; Aloy Patrick (January 2011). "3did: identification and classification of domain-based interactions of known three-dimensional structures". Nucleic Acids Res. England. 39 (Database issue): D718–23. doi:10.1093/nar/gkq962. PMC 3013799. PMID 20965963.
  2. Stein, A; Russell, R. B.; Aloy, P (2005). "3did: Interacting protein domains of known three-dimensional structure". Nucleic Acids Research. 33 (Database issue): D413–7. doi:10.1093/nar/gki037. PMC 539991. PMID 15608228.
  3. Mosca, R; Céol, A; Stein, A; Olivella, R; Aloy, P (2014). "3did: A catalog of domain-based interactions of known three-dimensional structure". Nucleic Acids Research. 42 (Database issue): D374–9. doi:10.1093/nar/gkt887. PMC 3965002. PMID 24081580.


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