TY - JOUR
T1 - DAPID
T2 - a 3D-domain annotated protein-protein interaction database.
AU - Chen, Yung Chiang
AU - Chen, Heng Chu
AU - Yang, Jinn-Moon
PY - 2006/1/1
Y1 - 2006/1/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=34250212118&partnerID=8YFLogxK
U2 - 10.11234/gi1990.17.2_206
DO - 10.11234/gi1990.17.2_206
M3 - Article
C2 - 17503393
AN - SCOPUS:34250212118
VL - 17
SP - 206
EP - 215
JO - Genome informatics. International Conference on Genome Informatics
JF - Genome informatics. International Conference on Genome Informatics
SN - 0919-9454
IS - 2
ER -