DAPID


17503393	DAPID: a 3D-domain annotated protein-protein interaction database. [PMID: 17503393] Chen YC, Chen HC, Yang JM. Abstract DAPID is a database of domain-annotated protein interactions inferred from three-dimensional (3D) interacting domains of protein complexes in the Protein Data Bank (PDB). The DAPID data model allows users to visualize 3D interacting domains, contact residues, and molecular details of any predicted protein-protein interactions. Our model derives these interactions by utilizing a new concept, called the ''3D-domain interologs'' which is similar to ''interologs''. In S. cerevisiae, there is 18.6% overlap between our predicted protein-protein interactions and ones in the DIP database. The mean correlation coefficient of the gene expression profiles of our predicted interactions is significantly higher than that for random pairs in S. cerevisiae. In addition, we find several novel interactions which are consistent with the functions of the proteins. The DAPID currently holds 1008 3D-interacting domain pairs and 101511 predicted 3D-domain annotated protein-protein interactions. It is available online at http://gemdock.life.nctu.edu.tw/dapid. Genome Inform. 2006:17(2) \| 8 Citations (from Europe PMC, 2025-04-05)

DAPID: a 3D-domain annotated protein-protein interaction database. [PMID: 17503393]

Chen YC, Chen HC, Yang JM.

DAPID is a database of domain-annotated protein interactions inferred from three-dimensional (3D) interacting domains of protein complexes in the Protein Data Bank (PDB). The DAPID data model allows users to visualize 3D interacting domains, contact residues, and molecular details of any predicted protein-protein interactions. Our model derives these interactions by utilizing a new concept, called the ''3D-domain interologs'' which is similar to ''interologs''. In S. cerevisiae, there is 18.6% overlap between our predicted protein-protein interactions and ones in the DIP database. The mean correlation coefficient of the gene expression profiles of our predicted interactions is significantly higher than that for random pairs in S. cerevisiae. In addition, we find several novel interactions which are consistent with the functions of the proteins. The DAPID currently holds 1008 3D-interacting domain pairs and 101511 predicted 3D-domain annotated protein-protein interactions. It is available online at http://gemdock.life.nctu.edu.tw/dapid.

Genome Inform. 2006:17(2) | 8 Citations (from Europe PMC, 2025-04-05)

URL:	http://gemdock.life.nctu.edu.tw/dapid
Full name:	3D-domain annotated protein-protein interaction database
Description:	The DAPID data model allows users to visualize 3D interacting domains, contact residues, and molecular details of any predicted protein-protein interactions. Our model derives these interactions by utilizing a new concept, called the ''3D-domain interologs'' which is similar to ''interologs''.
Year founded:	2006
Last update:
Version:
Accessibility:	Unaccessible
Country/Region:	China

Data type:	Protein
Data object:	Animal Archaea Bacteria Fungi Plant Virus
Database category:	Interaction Structure
Major species:	NA
Keywords:	3D-domain interologs 3D-domain annotated protein-protein interactions

University/Institution:	National Chiao Tung University
Address:	Institute of Bioinformatics, National Chiao Tung University Hsinchu, 30050, Taiwan.
City:	Taiwan
Province/State:	Taiwan
Country/Region:	China
Contact name (PI/Team):	Chen YC
Contact email (PI/Helpdesk):	smolljohn.bi93g@nctu.edu.tw

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Database Commons a catalog of worldwide biological databases