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3DID - 3D interacting domains
Please Cite:Amelie Stein, Arnaud Ceol & Patrick Aloy
3did: identification and classification of domain-based interactions of known three-dimensional structure
Nucleic Acids Res. 2011, 39, D718-723.
Older PublicationsAmelie Stein, Alejandro Panjkovich & Patrick Aloy
3did Update: domain-domain and peptide-mediated interactions of known 3D structure
Nucleic Acids Res. 2009, 37, D300-D304.
Amelie Stein, Robert B. Russell & Patrick Aloy
3did: interacting protein domains of known three-dimensional structure.
Nucleic Acids Res. 2005, 33, D413-D417.
The database of 3D Interaction Domains (3did) is a collection of domain-domain interactions in proteins for which high-resolution three-dimensional structures are known. 3did exploits structural information to provide critical molecular details necessary for understanding how interactions occur. It also offers an overview of how similar in structure are interactions between different members of the same protein family. The database also contains GO-based functional annotations and interactions between yeast proteins from large-scale interaction discovery studies.
Many transient interactions are mediated by a short linear peptide recognized by a globular domain, creating a relatively small contact interface. We searched the Protein Data Bank (PDB) for all occurrences of such interactions with motif patterns as described in the Eukaryotic Linear Motif database (ELM) (Stein & Aloy, PLoS ONE 2008) and included all these domain-motif interactions in 3did. Subsequently, we developed a method to identify peptide-mediated interactions based on structural features, and derived consensus motifs for those with sufficient non-redundant information (Stein & Aloy, PLoS Comput Biol 2010). Those instances where the motif is significantly enriched in model species interactomes are included in 3did.
Some statistical information on the current contents of 3did:
Details on domain-domain interactions (DDIs)
Details on domain-motif interactions