3did: a catalog of domain-based interactions of known three-dimensional structure

By Roberto Mosca, Arnaud Céol, Amelie Stein, Roger Olivella, Patrick Aloy. 2013

279 citations recorded by the source corpus.

The database of 3D interacting domains (3did, available online for browsing and bulk download at http://3did.irbbarcelona.org) is a catalog of protein–protein interactions for which a high-resolution 3D structure is known. 3did collects and classifies all structural templates of domain–domain interactions in the Protein Data Bank, providing molecular details for such interactions. 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 6 months.

Subfields: Molecular Biology, Pharmacology

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In Molecular Biology

Citations in the corpus

DockQ: A Quality Measure for Protein-Protein Docking Models (2016, background): “…in traditional structural biology and the structural genomics projects that aim at high-throughput complex structure determination [1], the latest statistics from 3did database [2] show that only 7% of the known protein interactions in humans have an associated experimental complex structure.”
End-to-End Learning on 3D Protein Structure for Interface Prediction (2018, methodology): “We also investigate structural-level pruning, removing any complexes in DIPS that share domain-domain interactions with DB5, as deﬁned in Mosca et al. [38].”
Towards a structurally resolved human protein interaction network (2021, background): “4,14 ) repository currently lists 7,625 predicted models based on homology of domains, a number similar to the 8,359 pairs listed having an experimentally determined model.”