My Ph.D.
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.
Yang*, "Template-based
protein structure prediction server,"
BMC Bioinformatics, in press, 2009
Paper accepted: F.-K. Lin, C.-L. Pan, J.-M.
Yang,
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)
[3D-BLAST
and fastSCOP:
Structural Genomics]
Our paper, Kappa-alpha plot
derived structural alphabet and BLOSUM-like substitution matrix for fast
protein structure database search, was published in Genome Biology. In this paper, we present a
novel protein structure database search tool, 3D-BLAST, that is useful
for analyzing novel structures and can return a ranked list of alignments.
This tool has the features of BLAST (for example, robust statistical basis,
search effective and reliable search capabilities) by using a kappa-alpha (k,
a) plot derived structural alphabet and a new substitution matrix. 3D-BLAST
searches over 12,000 protein structures in 1.2 seconds and yields good
results in zones with low sequence similarity.
[PPISearch and 3D-partner: Systems
Biology] We
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
homologous.
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
function. 3D-partner
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
similarity).
[FCEA: Bio-inspiration Computation Methods] Total cited number
of our papers, bio-inspiration computation methods (called FCEA) and their
applications, was over 250. FCEA
combines adaptive mutations and family competition to solve optimization
problems in widely differing fields (e.g. function optimization, constrained
optimization, and thin-film design, neural networks) and Bioinformatics
applications (e.g. protein-ligand interactions, protein-protein interaction
sites, protein folding, Microarray analysis, and QSAR model).
Awards
1.Tsai-Wei Shen
(沈再威, master student) and Chi-Hua
Tung (董其樺, master student) win the
prizes of 2004 and 2005 Best M.S. and Ph. D. Dissertation Award,
respectively, hosted by IICM (Institute of
Information & Computing Machinery).
2.We get the 2007
National Innovation Award, Yen-Fu Chen, Yu-Ju
Chen, and Jinn-Moon Yang, GEMDOCK: An Integrated Environment for
Computer-aided Drug Design and Its Applications. (GEMDOCK))