students, Chun-Chen Chen (陳俊辰)
and Chi-Hua Tung (董其樺), obtained Ph.D. Degree.
Paper accepted: C.-C. Chen, J.-K. Hwang and J.-M.
protein structure prediction server,"
BMC Bioinformatics, in press, 2009
Paper accepted: F.-K. Lin, C.-L. Pan, J.-M.
T.-J. ChuangandF.-C. Chen
"CAPIH: A Web interface for comparative analyses and visualization of
host-HIV protein-protein interactions," BMC Microbiology, pp. 9:164, 2009
Paper accepted: C.-C. Chen, C.-Y. Lin, Y.-S.
Lo, and J.-M. Yang*, "PPISearch: a web server for searching homologous
protein-protein interactions across multiple species," Nucleic Acids
Research, pp. W369-W375, 2009. (IF: 6.954)
[PPISearch and 3D-partner: Systems
derive a new concept, called the 3D-domain interologs
which is similar to interologs.
The 3D-domain interologs is defined
as Domain a (in chain A) interacts with domain b (in chain B) in a known 3D
complex, their inferring protein pair A' (containing domain a ) and B'
(containing domain b ) in the same species would be likely to interact with
each other if both protein pairs (A' and A as well as proteins B and B') are
3D-partner (3D-partner: a
web server to infer interacting partners and binding models), published
in Nucleic Acids Research, predicts interacting partners and binding
models by using 3D-domain
interologs through structure complexes and a knowledge-based scoring
utilizes IMPALA and PSI-BLAST to identify homologous structures and
interacting partners of a query protein sequence. These homologous structures
and interacting partners were evaluated by a new scoring function which
considered steric and special-bond matrices but
also the interfacial stability (couple-conserved residue score and template