Welcome to Yang, Jinn-Moon's Home Page

Welcome to Yang, Jinn-Moon's Home Page

Professor and Director

Drug Design and Systems Biology Laboratory


Department of Biological Science and Technology

Institute of Bioinformatics, National Chiao Tung University


Address: 75 PO-Ai Street, Hsinchu, Taiwan, 30050

Office & Lab : 308 and 304 (Lab) in Experiment Building
Tel: 886-3-5712121 ext.56942; Fax: 886-3-5729288
E-mail: moon@faculty.nctu.edu.tw


RESUME & Research Profile (in Chinese and English)

The World of Drug Discovery, Function (Structural) Bioinformatics And Systems Biology.


Let dreams COME TURE.


News and Highlights

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. Chuang and F.-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)

Co-advised Ph.D. student, Yen-Wei Chu (Dr. 朱彥煒), started Assistant Professor at Institute of Bioinformatics, National Chung Hsing University, Aug. 2008.


[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.

fastSCOP (fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies, published in NAR) rapidly identifies the structural domains and determines the evolutionary superfamilies of a query protein structure. fastSCOP uses 3D-BLAST to scan quickly a large structural classification database and MAMMOTH, a detailed structural alignment tool, is adopted to refine domain boundaries and to identify evolutionary superfamilies.


[GEMDOCK: Drug Discovery] Total cited number of our papers, well-developed docking tool (GEMDOCK) and its applications, was over 100. Based on the ability and flexibility of GEMDOCK, we have successfully cooperated over seven Labs, such as NHRI, Prof Hsu TA (Inhibitors of avian influenza virus neuraminidases); Prof. Wang WC (Inhibitors of helicobacter pylori shikimate kinase), Prof MAO JT (secondary vitamin D3 binding site of milk beta-lactoglobulin); Prof. Yang YS (Substrates of sulfotransferase and hydantoinase); Prof. Yuan CJ (Substrates of amine oxidase); Prof. Yang YL (Inhibitors of envelop protein of dengue virus); and Prof. Liao KW (peptide-binding motifs of MHC class I). We also cooperated with Prof. Hsu on data fusion for virtual screening. (download)


[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).




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))