Home Query Domains & Motifs Browse Query interactions PDB & GO terms InterPreTS

3DID - 3D interacting domains

The current version of 3did is based on Pfam release 24 and HMMER version 3(beta).

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 Publications

Amelie 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.

Biological Background

Domain-Domain Interactions

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.

Domain-Motif Interactions

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.

  1. Amelie Stein & Patrick Aloy
    Contextual Specificity in Peptide-Mediated Protein Interactions
    PLoS ONE 3(7): e2524, 2008.
  2. Amelie Stein & Patrick Aloy
    Novel Peptide-Mediated Interactions Derived from High-Resolution 3-Dimensional Structures
    PLoS Comput Biol 6(5): e1000789, 2010.

Some statistical information on the current contents of 3did:

4302 unique Pfam domains participating in domain-domain interactions
6260 unique Pfam domain-domain-interactions
3535 domains annotated with molecular_function GO-terms
2662 domains annotated with biological_process GO-terms
1368 domains annotated with cellular_component GO-terms
175144 domain-domain interactions of known 3D structure
174006 Proteins

Details on domain-domain interactions (DDIs)

857 distinct types of DDIs that occur in intrachain interactions
4427 distinct types of DDIs that occur in interchain interactions
976 distinct DDIs are observed both inter- and intrachain

Details on domain-motif interactions

1663 structures of domain-motif interactions
114 linear motifs in interactions of known 3d structure
63 domains binding motifs

Pronunciation

3-d-i-d

Help

Valid HTML 4.01!