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DDIB - Database of Domain Interactions and Binding

NAR Molecular Biology Database Collection entry number 659
Yu, X.J.1, Chen, M.2, Lin, J.C.1, Li, X.3, Shi, T.L.1, He, W.Z.2 and Li, Y.X.1,2
1Bioinformatics Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
2Shanghai Center for Bioinformation Technology, Shanghai 200235, China
3Department of Computer Science, Shanghai Normal University, Shanghai 200234, China

Database Description

Protein domains, modules of amino acid sequence with specific evolutionarily conserved motifs, are the structural or functional units that participate in intermolecular interactions. Information about domain interactions has been accumulated, but are buried in literatures or scattered in various laboratories, thus, hard for users to find them.

The Database of Domain Interactions and Bindings (DDIB) collects information about domain-domain interactions and domain interactions with biological molecules such as nucleotides, peptides, inorganic ions, phospholipids. Some data were extracted By Natural Language Processing (NLP) method from publication abstracts included in MEDLINE, and some were collected from other public databases, research laboratories and individual scientists. In addition, DDIB includes many putative domain-domain interactions inferred from documented protein-protein interactions. To provide comprehensive knowledge of a domain, DDIB also includes relevant information from PFAM database, GO and KEGG. DDIB is freely accessible from


This project was funded in part by the State Key Program of Basic Research of China (No. 001CB510209) and the 863 Hi-Tech Program (No. 2003AA231011).

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