title: DAPID: a 3D-domain annotated protein-protein interaction database.
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.
authors.affiliation: Institute of Bioinformatics, National Chiao Tung University Hsinchu, 30050, Taiwan. smolljohn.bi93g@nctu.edu.tw
authors.forename: Yung-Chiang
authors.initials: YC
authors.lastname: Chen
authors.forename: Heng-Chu
authors.initials: HC
authors.lastname: Chen
authors.forename: Jinn-Moon
authors.initials: JM
authors.lastname: Yang
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D003196:Computer Graphics; D030562:Databases, Protein; D020869:Gene Expression Profiling; D008954:Models, Biological; D008969:Molecular Sequence Data; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000145:classification / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D012680:Sensitivity and Specificity; D020539:Sequence Analysis, Protein; D017386:Sequence Homology, Amino Acid; D014584:User-Computer Interface
chemical_list: D011506:Proteins; D029701:Saccharomyces cerevisiae Proteins