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科技部產學小聯盟:
生技及醫藥服務平台於生技產品開發推廣聯盟

  • [2016/07] 與奎克生技光電簽署產學合作計畫(240萬)
  • [2015/07] 與高醫及奎克生技完成 30 例登革熱病人 miRNA 分析
  • 與三總李日清主任進行頭頸癌預後 Biomarker 合作
  • 與中國醫、三總李日清主任進行頭頸癌血液中早期 Biomarker 合作
  • [2016/01/05] 舉辦創新藥物開發-市場策略前瞻生技醫藥研討會
  • [2015/12] 月底與奎克生技光電簽署合作備忘錄
  • [2015/11/25] 交大-台灣共振波 產學合作會議
  • [2015/11] 月底與台灣神隆續約產學合作
  • [2015/11/23] 交大-奎克生技光電 產學合作會議
  • [2015/10/26] 交大-宣捷生技 產學合作交流技術研討會
  • [2015/10/13] 啟動大數據並共創幹細胞大未來 宣捷生技與交大攜手產學合作[新聞連結]
  • [2015/10/20] 交大-華聯生技-三軍總醫院 產學醫技術研討會
  • [2015/08/03] 葡萄王生技公司參訪交流
  • [2015] 生技及醫藥應用平台於生技產品開發聯盟-歡迎華聯生技高錦男總經理蒞臨本校參訪
楊進木 (Jinn-Moon Yang)

Professor
Drug Design and Systems Biology Laboratory
Department of Biological Science and Technology
Institute of Bioinformatics & Systems Biology, National Chiao Tung University

Address: 75 Po-Ai Street, Hsinchu, Taiwan, 30068
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 in Chinese

Research Overview:

    I (Jinn-Moon Yang) am a full professor of Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Taiwan. Our primary goal is to study inhibitor-protein-pathway-disease relationships in a cell. The major research areas include drug discovery, structural bioinformatics, and systems biology. I published over 70 SCI papers on some journals, such as Genome Biology, Nucleic Acids Research, PLOS Computational Biology, Scientific Reports, and Bioinformatics. My h-index is 28 and 20 based on Google scholar and ISI Web of Knowledge, respectively. Based on ISI and Google scholar databases, total numbers of citations are over 1,100 and 2,600, respectively. Our team has developed a molecular docking (GEMDOCK) and site-moiety map (SiMMap) for molecular interaction (e.g., protein-ligand and protein-protein) mechanism analysis. My team achieved successful results on a fast protein structure search tool (3D-BLAST) which is as fast as BLAST and has the features of BLAST. We are the first team to introduce protein-protein interacting family and protein-ligand family which is similar to the concept of the protein or gene family. I also joined the editorial board of PLoS ONE.

Selected Papers

  1. Lin, C. Y., Lee, T. L., Chiu, Y. Y., Lin, Y. W., Lo, Y. S., Lin, C. T., and Yang, J. M.* (2015) Module organization and variance in protein-protein interaction networks, Scientific Reports, doi: 10.1038/srep09386.
  2. Chiu, Y. Y., Lin, C. T., Huang, J. W., Hsu, K. C., Tseng, J. H., You, S. R., and Yang, J. M.* (2013) KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms, Nucleic Acids Research, D430-D440.
  3. Hsu, K. C., Cheng, W. C., Chen, Y. F., Wang, W. C., and Yang, J. M.* (2013) Pathway-based screening strategy for multitarget inhibitors of diverse proteins in metabolic pathways, PLOS Computational Biology 9, e1003127.
  4. Lin, C. Y., Lin, Y. W., Yu, S. W., Lo, Y. S., and Yang, J. M.* (2012) MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates, Nucleic Acids Research 40, W263-W270.
  5. Lee, C. C., Maestre‐Reyna, M., Hsu, K. C., Wang, H. C., Liu, C. I., Jeng, W. Y., Lin, L. L., Wood, R., Chou, C. C., Yang, J. M., and Wang, A. H. (2014) Crowning Proteins: Modulating the Protein Surface Properties using Crown Ethers, Angewandte Chemie International Edition, 13054–13058.
  6. Chu, C. H., Wang, L. Y., Hsu, K. C., Chen, C. C., Cheng, H. H., Wang, S. M., Wu, C. M., Chen, T. J., Li, L. T., Liu, R. Hung, C. L., Yang, J. M.*, Kung, H. J.*, and Wang, W. C.* (2014) KDM4B as a target for prostate cancer: structural analysis and selective inhibition by a novel inhibitor, Journal of Medicinal Chemistry, 5975-5985.
  7. Tung, C. H., Huang, J. W., and Yang, J. M.* (2007) Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database, Genome Biology 8.
  8. Chen, Y. C., Lo, Y. S., Hsu, W. C., and Yang, J. M.* (2007) 3D-partner: a web server to infer interacting partners and binding models, Nucleic Acids Research 35, W561-W567.
  9. Chen, C. C., Hwang, J. K., and Yang, J. M.* (2006) (PS)(2): protein structure prediction server, Nucleic Acids Research 34, W152-W157.
  10. Yang, J. M.*, Chen, Y. F., Shen, T. W., Kristal, B. S., and Hsu, D. F. (2005) Consensus scoring criteria for improving enrichment in virtual screening, Journal of Chemical Information and Modeling 45, 1134-1146.
  11. Yang, J. M.*, and Chen, C. C. (2004) GEMDOCK: A generic evolutionary method for molecular docking, Proteins-Structure Function and Bioinformatics 55, 288-304.

Complete Journal Papers

  1. Hsu, K. C., Sung, T. Y., Lin, C. T., Chiu, Y. Y., Hsu, J. T., Hung, H. C., Sun, C. M., Barve, I., Chen, W. L., Huang, W. C., Huang, C. T., Chen, C. H., and Yang, J. M. (2015) Anchor-based classification and type-C inhibitors for tyrosine kinases, Scientific Reports, doi: 10.1038/srep10938.
  2. Lin, C. Y., Lee, T. L., Chiu, Y. Y., Lin, Y. W., Lo, Y. S., Lin, C. T., and Yang, J. M.* (2015) Module organization and variance in protein-protein interaction networks, Scientific Reports, doi: 10.1038/srep09386.
  3. Lo, Y. S., Huang, S. H., Luo, Y. C., Lin, C. Y., and Yang, J. M.* (2015) Reconstructing genome-wide protein-protein interaction networks using multiple strategies with homologous mapping, Plos One 10, e0116347.
  4. Lee, J. C., Lai, W. S., Ju, D. T., Chu, Y. H., and Yang, J. M. (2015) Diode laser assisted minimal invasive sphenoidotomy for endoscopic transphenoidal pituitary surgery: Our technique and results, Lasers in Surgery and Medicine 47, 239-242.
  5. Lee, G. C., Lin, C. H., Tao, Y. C., Yang, J. M. , Hsu, K. C., Huang, Y. J., Huang, S. H., Kung, P. J., Chen, W. L., Wang, C. M., Wu, Y. R., Chen, C. M., Lin, J. Y., Hsieh-Li, H. M., and Lee-Chen, G. J. (2015) The potential of lactulose and melibiose, two novel trehalase-indigestible and autophagy-inducing disaccharides, for polyQ-mediated neurodegenerative disease treatment, Neurotoxicology, doi: 10.1016/j.neuro.2015.1003.1009.
  6. Lee, C. C., Maestre‐Reyna, M., Hsu, K. C., Wang, H. C., Liu, C. I., Jeng, W. Y., Lin, L. L., Wood, R., Chou, C. C., Yang, J. M., and Wang, A. H. (2014) Crowning Proteins: Modulating the Protein Surface Properties using Crown Ethers, Angewandte Chemie International Edition, 13054–13058.
  7. Chu, C. H., Wang, L. Y., Hsu, K. C., Chen, C. C., Cheng, H. H., Wang, S. M., Wu, C. M., Chen, T. J., Li, L. T., Liu, R. Hung, C. L., Yang, J. M.*, Kung, H. J.*, and Wang, W. C.* (2014) KDM4B as a target for prostate cancer: structural analysis and selective inhibition by a novel inhibitor, Journal of Medicinal Chemistry, 5975-5985.
  8. Chiu, Y. Y., Tseng, J. H., Liu, K. H., Lin, C. T., Hsu, K. C. and Yang, J. M.* (2014) Homopharma: A new concept for exploring the molecular binding mechanisms and drug repurposing, BMC Genomics, Suppl 7:S11. (Best paper award in The 13th International Conference on Bioinformatics)
  9. Wang, H. C., Ho, C. H., Hsu, K. C., Yang, J. M. and Wang, A.H. (2014) DNA mimic proteins: functions, structures, and bioinformatic analysis, Biochemistry, 2865-2874.
  10. Wang, H. C., Hsu, K. C., Yang, J. M.Wu, M. L., Ko, T. P., Lin, S. R. and Wang, A. H. (2014) Staphylococcus aureus protein SAUGI acts as a uracil-DNA glycosylase inhibitor, Nucleic Acids Research, 1354-1364.
  11. Ma, N., Lai, C.-S., Chung, C.-H., Yang, J.-M., Hsu, K.-C., Chen, C.-Y., Chung, T.-S., Li, S., Ho, C.-T., and Pan, M.-H. (2014) 5-Demethyltangeretin is more potent than tangeretin in inhibiting dimethylbenz (a) anthracene (DMBA)/12-O-tetradecanoylphorbol-13-acetate (TPA)-induced skin tumorigenesis, Journal of Functional Foods, 528-537.
  12. Tsai, W. C., Yang, J. M., Liu, S. C., Chu, Y. H., Lai, W. S., Lin, Y. S., and Lee, J. C. (2014) Management of different kinds of head and neck defects with the submental flap for reconstruction, European Archives of Oto-Rhino-Laryngology, DOI 10.1007/s00405-00014-03461-00400.
  13. Liu, I. H., Lo, Y. S., and Yang, J. M.* (2013) Genome-wide structural modelling of TCR-pMHC interactions, BMC Genomics, Suppl 5:S5.
  14. Chiu, Y. Y., Lin, C. T., Huang, J. W., Hsu, K. C., Tseng, J. H., You, S. R., and Yang, J. M.* (2013) KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms, Nucleic Acids Research, D430-D440.
  15. Hsu, K. C., Cheng, W. C., Chen, Y. F., Wang, W. C., and Yang, J. M.* (2013) Pathway-based screening strategy for multitarget inhibitors of diverse proteins in metabolic pathways, PLOS Computational Biology 9, e1003127.
  16. Hsu, K. C., Hung, H. C., Horng, J. T., Fang, M. Y., Chang, C. Y., Li, L. T., Chen, I. J., Chen, Y. C., Chou, D. L., Chang, C. W., Hsieh, H. P., Yang, J. M.*, and J. T., Hsu*. (2013) Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors, PLoS ONE 8, e56704.
  17. Lin, C. Y., Chen, Y. C., Lo, Y. S., and Yang, J. M.* (2013) Inferring homologous protein-protein interactions through pair position specific scoring matrix, BMC Bioinformatics 14, Suppl 2:S11.
  18. Chen, Y. J., Kay, N., Yang, J. M., Lin, C. T., Chang, H. L., Wu, Y. C., Fu, C. F., Chang, Y., Lo, S., Hou, M. F., Lee, Y. C., Hsieh, Y. C., and Yuan, S. S. (2013) Total Synthetic Protoapigenone WYC02 Inhibits Cervical Cancer Cell Proliferation and Tumour Growth through PIK3 Signaling Pathway, Basic & Clinical Pharmacology & Toxicology, 8-18.
  19. Lin, C. H., Chang, T. C., Das, A., Fang, M. Y., Hung, H. C., Hsu, K. C., Yang, J. M., M, v. I., Mong, K. K., Hsu, T. A., and Lin, C. C. (2013) Synthesis of acylguanidine zanamivir derivatives as neuraminidase inhibitors and the evaluation of their bio-activities, Organic & Biomolecular Chemistry 11, 3943-3948.
  20. Chen, S. H., Lin, S. W., Lin, S. R., Liang, P. H., and Yang, J. M.* (2013) Moiety-linkage map reveals selective non-bisphosphonate inhibitors of human geranylgeranyl diphosphate synthase, Journal of Chemical Information and Modeling, 2299-2311.
  21. Lin, C. Y., Lin, Y. W., Yu, S. W., Lo, Y. S., and Yang, J. M.* (2012) MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates, Nucleic Acids Research 40, W263-W270.
  22. Huang, J. W., Lin, W. F., and Yang, J. M.* (2012) Antigenic sites of H1N1 influenza virus hemagglutinin revealed by natural isolates and inhibition assays, Vaccine 30, 6327-6337.
  23. Hsu, S. C., Chang, C. P., Tsai, C. Y., Hsieh, S. H., Wu-Hsieh, B. A., Lo, Y. S., and Yang, J. M. (2012) Steric recognition of T-cell receptor contact residues is required to map mutant epitopes by immunoinformatical programmes, Immunology 136, 139-152.
  24. Hsu, K. C., Cheng, W. C., Chen, Y. F., Wang, H. J., Li, L. T., Wang, W. C., and Yang, J. M.* (2012) Core site-moiety maps reveal inhibitors and binding mechanisms of orthologous proteins by screening compound libraries, PLoS ONE 7, e32142.
  25. Hsu, K. C., Chen, Y. F., and Yang, J. M.* (2012) GemAffinity: a scoring function for predicting binding affinity and virtual screening, International Journal of Data Mining and Bioinformatics 6, 27-41.
  26. Chiu, Y. Y., Lin, C. Y., Lin, C. T., Hsu, K. C., Chang, L. Z., and Yang, J. M.* (2012) Space-related pharma-motifs for fast search protein binding motifs and polypharmacological targets, BMC Genomics 13, Suppl 7:S21.
  27. Cheng, W. C., Chen, Y. F., Wang, H. J., Hsu, K. C., Lin, S. C., Chen, T. J., Yang, J. M.*, and Wang, W. C. (2012) Structures of Helicobacter pylori shikimate kinase reveal a selective inhibitor-induced-fit mechanism, PLoS ONE 7, e33481.
  28. Chang, K. M., Chen, S. H., Kuo, C. J., Chang, C. K., Guo, R. T., Yang, J. M., and Liang, P. H. (2012) Roles of amino acids in the Escherichia coli octaprenyl diphosphate synthase active site probed by structure-guided site-directed mutagenesis, Biochemistry 51, 3412-3419.
  29. Tsai, C. C., Liu, H. F., Hsu, K. C.,Yang, J. M., Chen, C. P., Liu, K. K., Hsu, T. S., and Chao, J. I. (2011) 7-Chloro-6-piperidin-1-yl-quinoline-5,8-dione (PT-262), a novel ROCK inhibitor blocks cytoskeleton function and cell migration, Biochemical Pharmacology 81, 856-865.
  30. Liu, I. H., Lo, Y. S., and Yang, J. M.* (2011) PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes, Nucleic Acids Research 39, W254-W260.
  31. Huang, J. W., and Yang, J. M.* (2011) Changed epitopes drive the antigenic drift for influenza A (H3N2) viruses, BMC Bioinformatics 12, Suppl 1:S31.
  32. Hsu, K. C., Chen, Y. F., Lin, S. R., and Yang, J. M.* (2011) iGEMDOCK: a graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis, BMC Bioinformatics 12, Suppl 1:S33.
  33. Clinciu, D. L., Yang, J. M., Hsu, K. C., Lo, C. C., Wallace, S., and Yu, H. C. (2011) The relevance of protein-ligand interaction profiles in computer-aided novel compound design and applications, Current Bioinformatics 6, 383-388.
  34. Lo, Y. S., Lin, C. Y., and Yang, J. M.* (2010) PCFamily: a web server for searching homologous protein complexes, Nucleic Acids Research 38, W516-W522.
  35. Lo, Y. S., Chen, Y. C., and Yang, J. M.* (2010) 3D-interologs: an evolution database of physical protein- protein interactions across multiple genomes, BMC Genomics 11, Suppl 3:S7.
  36. Liu, K. P., Hsu, K. C., Huang, J. W., Chang, L. S., and Yang, J. M.* (2010) ATRIPPI: An atom-residue preference scoring function for protein-protein interactions, International Journal on Artificial Intelligence Tools 19, 251-266.
  37. Clinciu, D. L., Chen, Y. F., Ko, C. N., Lo, C. C., and Yang, J. M.* (2010) TSCC: Two-Stage Combinatorial Clustering for virtual screening using protein-ligand interactions and physicochemical features, BMC Genomics 11, Suppl 4:S26.
  38. Chin, K. H., Lee, Y. C., Tu, Z. L., Chen, C. H., Tseng, Y. H., Yang, J. M.*, Ryan, R. P., McCarthy, Y., Dow, J. M., Wang, A. H. J., and Chou, S. H. (2010) The c-AMP receptor-like protein clp is a novel c-di-gmp receptor linking cell-cell signaling to virulence gene expression in xanthomonas campestris, Journal of Molecular Biology 396, 646-662.
  39. Chen, Y. F., Hsu, K. C., Lin, S. R., Wang, W. C., Huang, Y. C., and Yang, J. M.* (2010) SiMMap: a web server for inferring site-moiety map to recognize interaction preferences between protein pockets and compound moieties, Nucleic Acids Research 38, W424-W430.
  40. Lin, F. K., Pan, C. L., Yang, J. M., Chuang, T. J., and Chen, F. C. (2009) CAPIH: A web interface for comparative analyses and visualization of host-HIV protein-protein interactions, BMC Microbiology 9, 164.
  41. Hung, H. C., Tseng, C. P., Yang, J. M., Ju, Y. W., Tseng, S. N., Chen, Y. F., Chao, Y. S., Hsieh, H. P., Shih, S. R., and Hsu, J. T. A. (2009) Aurintricarboxylic acid inhibits influenza virus neuraminidase, Antiviral Research 81, 123-131.
  42. Huang, J. W., King, C. C., and Yang, J. M.* (2009) Co-evolution positions and rules for antigenic variants of human influenza A/H3N2 viruses, BMC Bioinformatics 10, Suppl 1:S41.
  43. Chen, C. C., Lin, C. Y., Lo, Y. S., and Yang, J. M.* (2009) PPISearch: a web server for searching homologous protein-protein interactions across multiple species, Nucleic Acids Research 37, W369-W375.
  44. Chen, C. C., Hwang, J. K., and Yang, J. M.* (2009) (PS)(2)-v2: template-based protein structure prediction server, BMC Bioinformatics 10, 10:366.
  45. Yao, Y. Y., Shrestha, K. L., Wu, Y. J., Tasi, H. J., Chen, C. C., Yang, J. M., Ando, A., Cheng, C. Y., and Li, Y. K. (2008) Structural simulation and protein engineering to convert an endo-chitosanase to an exo-chitosanase, Protein Engineering Design & Selection 21, 561-566.
  46. Yang, M. C., Guan, H. H., Yang, J. M., Ko, C. N., Liu, M. Y., Lin, Y. H., Huang, Y. C., Chen, C. J., and Mao, S. J. T. (2008) Rational design for crystallization of beta-lactoglobulin and Vitamin D(3) complex: revealing a secondary binding site, Crystal Growth & Design 8, 4268-4276.
  47. Yang, M. C., Guan, H. H., Liu, M. Y., Lin, Y. H.,Yang, J. M., Chen, W. L., Chen, C. J., and Mao, S. J. T. (2008) Crystal structure of a secondary vitamin D(3) binding site of milk beta-lactoglobulin, Proteins-Structure Function and Bioinformatics 71, 1197-1210.
  48. Yang, C. Y., Chang, C. H., Yu, Y. L., Lin, T. C. E., Lee, S. A., Yen, C. C., Yang, J. M., Lai, J. M., Hong, Y. R., Tseng, T. L., Chao, K. M., and Huang, C. Y. F. (2008) PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database, Bioinformatics 24, I14-I20.
  49. Chiu, Y. Y., Hwang, J. K., and Yang, J. M.* (2008) Soft energy function and generic evolutionary method for discriminating native from nonnative protein conformations, Journal of Computational Chemistry 29, 1364-1373.
  50. Chang, Y. L., Tsai, H. K., Kao, C. Y., Chen, Y. C., Hu, Y. J., and Yang, J. M.* (2008) Evolutionary conservation of DNA-contact residues in DNA-binding domains, BMC Bioinformatics 9, Suppl 6:S3.
  51. Yang, J. M., Chen, Y. F., Tu, Y. Y., Yen, K. R., and Yang, Y. L. (2007) Combinatorial computational approaches to identify tetracycline derivatives as flavivirus inhibitors, PLoS ONE 2, e428.
  52. Tung, C. H., and Yang, J. M.* (2007) fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies, Nucleic Acids Research 35, W438-W443.
  53. Tung, C. H., Huang, J. W., and Yang, J. M.* (2007) Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database, Genome Biology 8.
  54. Chen, Y. C., Lo, Y. S., Hsu, W. C., and Yang, J. M.* (2007) 3D-partner: a web server to infer interacting partners and binding models, Nucleic Acids Research 35, W561-W567.
  55. Yang, J. M.*, and Tung, C. H. (2006) Protein structure database search and evolutionary classification, Nucleic Acids Research 34, 3646-3659.
  56. Chen, C. C., Hwang, J. K., and Yang, J. M.* (2006) (PS)(2): protein structure prediction server, Nucleic Acids Research 34, W152-W157.
  57. Yang, J. M.*, and Shen, T. W. (2005) A pharmacophore-based evolutionary approach for screening selective estrogen receptor modulators, Proteins-Structure Function and Bioinformatics 59, 205-220.
  58. Yang, J. M.*, Chen, Y. F., Shen, T. W., Kristal, B. S., and Hsu, D. F. (2005) Consensus scoring criteria for improving enrichment in virtual screening, Journal of Chemical Information and Modeling 45, 1134-1146.
  59. Yang, J. M.*, and Chen, C. C. (2004) GEMDOCK: A generic evolutionary method for molecular docking, Proteins-Structure Function and Bioinformatics 55, 288-304.
  60. Yang, J. M.* (2004) Development and evaluation of a generic evolutionary method for protein-ligand docking, Journal of Computational Chemistry 25, 843-857.
  61. Tsai, H. K., Yang, J. M., Tsai, Y. F., and Kao, C. Y. (2004) Some issues of designing genetic algorithms for traveling salesman problems, Soft Computing 8, 689-697.
  62. Tsai, H. K., Yang, J. M., Tsai, Y. F., and Kao, C. Y. (2004) An evolutionary algorithm for large traveling salesman problems, IEEE Transactions on Systems Man and Cybernetics Part B-Cybernetics 34, 1718-1729.
  63. Tsai, H. K., Yang, J. M.*, Tsai, Y. F., and Kao, C. Y. (2004) An evolutionary approach for gene expression patterns, IEEE Transactions on Information Technology in Biomedicine 8, 69-78.
  64. Yu, C. S., Wang, J. Y., Yang, J. M., Lyu, P. C., Lin, C. J., and Hwang, J. K. (2003) Fine-grained protein fold assignment by support vector machines using generalized npeptide coding schemes and jury voting from multiple-parameter sets, Proteins-Structure Function and Bioinformatics 50, 531-536.
  65. Tsai, H. K., Yang, J. M., Tsai, Y. F., and Kao, C. Y. (2003) Heterogeneous selection genetic algorithms for traveling salesman problems, Engineering Optimization 35, 297-311.
  66. Lin, E. S., Yang, J. M., and Yang, Y. S. (2003) Modeling the binding and inhibition mechanism of nucleotides and sulfotransferase using molecular docking, Journal of the Chinese Chemical Society 50, 655-663.
  67. Chuang, C. C., Chen, C. Y., Yang, J. M., Lyu, P. C., and Hwang, J. K. (2003) Relationship between protein structures and disulfide bonding patterns, Proteins-Structure Function and Genetics 53, 1-5.
  68. Chu, Y. W., and Yang, J. M.* (2003) Finding regularity in various types of secondary protein structures, Journal of Information Science and Engineering 19, 943-952.
  69. Yang, J. M.*, Tsai, C. H., Hwang, M. J., Tsai, H. K., Hwang, J. K., and Kao, C. Y. (2002) GEM: A Gaussian evolutionary method for predicting protein side-chain conformations, Protein Science 11, 1897-1907.
  70. Yang, J. M.*, Lin, C. J., and Kao, C. Y. (2002) A robust evolutionary algorithm for global optimization, Engineering Optimization 34, 405-425.
  71. Yang, J. M.*, and Kao, C. Y. (2001) Efficient evolutionary algorithm for the thin-film synthesis of inhomogeneous optical coatings, Applied Optics 40, 3256-3267.
  72. Yang, J. M.*, and Kao, C. Y. (2001) An evolutionary algorithm for the synthesis of multilayer coatings at oblique light incidence, Journal of Lightwave Technology 19, 559-570.
  73. Yang, J. M.*, and Kao, C. Y. (2001) A robust evolutionary algorithm for training neural networks, Neural Computing & Applications 10, 214-230.
  74. Yang, J. M.*, Horng, J. T., Lin, C. J., and Kao, C. Y. (2001) Optical coating designs using the family competition evolutionary algorithm, Evolutionary Computation 9, 421-443.
  75. Yang, J. M.*, and Kao, C. Y. (2000) Integrating adaptive mutations and family competition into genetic algorithms as function optimizer, Soft Computing 4, 89-102.
  76. Yang, J. M.*, and Kao, C. Y. (2000) A family competition evolutionary algorithm for automated docking of flexible ligands to proteins, IEEE Transactions on Information Technology in Biomedicine 4, 225-237.
  77. Yang, J. M.*, and Kao, C. Y. (2000) Flexible ligand docking using a robust evolutionary algorithm, Journal of Computational Chemistry 21, 988-998.
  78. Yang, J. M.*, Horng, J. T., and Kao, C. Y. (2000) A genetic algorithm with adaptive mutations and family competition for training neural networks, International Journal of Neural Systems 10, 333-352.

Patents

  1. Wang, W. C., Cheng, W. C., and Yang, J. M. Method of inhibiting the growth of Helicobacter pylori. US patent 8175860, 2012/5/8
  2. 楊進木、許凱程、黃兆祺、陳文亮、趙瑞益、黃文傑。一種專一性表皮生長因子接受器之選擇性抑制劑、其醫藥組成物及其用途。中華民國專利:發明第 I536987 號,2016/06/11。
  3. 楊進木、許凱程、宋姿瑩、林伸融、王雲銘、許光美、林欣平、劉婉婷。蛋白質激酶之選擇性抑制劑、其醫藥組成物及其用途。中華民國專利:發明第 I538914 號,2016/06/21。
楊進木
(Jinn-Moon Yang)

Postdoctoral Researchers:

Assistants:

Ph.D. Students:

MD. Ph.D. Students:

Master Students:

Undergraduate Students:


PI

楊進木 (Jinn-Moon Yang)
  • Computer-aided drug design
  • Systems Biology
  • Structural Bioinformatics
  • Machine Learning
  • Editorial Boards of PLoS ONE and Frontiers in Bioinformatics and Computational Biology
  • Member of Bioinformatics and Systems Biology Society Taiwan
  • Professor, Institute of Systems Biology Bioinformatics, National Chiao-Tung University
  • Win the 2007 National Innovation Award, iGEMDOCK: A graphical-automatic drug system for docking, screening and post-analysis
  • Win outstanding Research Award at the National Chiao-Tung University (2006, 2009-2014)
  • The total number of citations over 2,200 and my H-index is 26 based on Google scholar index

Postdoctoral Researchers

林峻宇 (Chun-Yu Lin)
Major Fields in BS: Biological Technology
Molecular interaction networks for tumorigenesis and metastasis
Journal paper: 7 papers
E-mail: m75225@gmail.com
曾郁堯 (Yu-Yao Tseng; York)
Major Fields in BS: Life Sciences
The development of effective cosmeceuticals and nutraceuticals
Journal paper: 4 papers
E-mail: york@nctu.edu.tw
楊文賓 (Wen-Bin Yang)
Major Fields in BS: Bioagricultural Science and Technology
Drug design and repurposing
Journal paper: 9 papers
E-mail: geniusbing@gmail.com
詹秀倩 (Hsiu-Chien Chan)
Major Fields in BS: Structural Biology and Biological Science
Drug repurposing & Protein structure
Journal paper: 23 papers
E-mail: sandra120978@gmail.com

Assistants

齊婉葶 (Wan-Ting Chi)
Administrative Assistant
E-mail: momochi1230@gmail.com
宋姿瑩 (Tzu-Ying Sung)
Research Assistant
Major Fields in BS: Food Science
Kinsae: Type-S inhibitor
E-mail: tzyying34@gmail.com
羅永淳 (Yong-Chun Luo)
Research Assistant
Major Fields in BS: Biological Technology
Diabetes
E-mail: jimmy22452736@yahoo.com.tw
賴玫伶 (Mei-Ling Lai)
Research Assistant
Major Fields in BS: Biological Technology
Drug repurposing
E-mail: gjh932089@hotmail.com
許惠惠 (Hui-Hui Hsu)
Research Assistant
Major Fields in BS: Biological Technology
Phosphorylation Pathway Disease (FHA domain)
E-mail: olgaxu510@gmail.com
楊方琪 (Fung-Chi Yang)
Research Assistant
Major Fields in BS: Biological Technology
Biological Technology
E-mail: moonci33@gmail.com

Ph.D. Students

黃星翰 (Sing-Han Huang)
Major Fields in BS: Biochemical Science and Technology
Human Brain Aging and Neurodegeneration Disease
Journal paper: 1 paper
E-mail: gb921.tw@gmail.com
莊佾軒 (Yi-Shen Chung)
Major Fields in BS: Computer Science
Molecular interaction networks for tumorigenesis and metastasisvirus
E-mail: newyvmp40fm06@gmail.com
洪瓊慧 (Chiung-Hui Hung)
Major Fields in BS: Life Science
Journal paper: 3 papers
Nikhil Pathak
Major Fields in BS: Pharmacy
Drug Design for Pathogenic and infectious Diseases - Dengue
E-mail: nikhilpathak27@gmail.com
許彥超 (Yen-Chao Hsu; Jerry)
Major Fields in BS: Computer Science
Protein-Ligand Family
E-mail: yenchaohsu@gmail.com

MD. Ph.D. Students

賴文森 (Wen-Sen Lai)
Major Fields in BS: Department of Otolaryngology, Taichung Armed forces General Hospital
General otolaryngology
Journal paper: 22 papers

Master Students

李容羽 (Jung-Yu Lee)
Major Fields in BS: Animal Science
Molecular interaction networks for tumorigenesis and metastasis
E-mail: leejungyu1012@gmail.com
巫思穎 (Szu-Ying Wu)
Major Fields in BS: Microbiology
Drug-target disease profiling - L1000 database
Drug Design for Pathogenic and infectious Diseases - Dengue virus
E-mail: winnie40424@yahoo.com.tw
劉威廷 (Wei-Ting Liu)
Major Fields in BS: Food sciences
E-mail: ga20060102658@gmail.com
李力渝 (Li-Yu Li)
Major Fields in BS: Food Science
Flavor of meat discussion from enzyme produce
E-mail: tso2158581@gmail.com
郭超望 (Chao-Wang Kuo)
Major Fields in BS: Medical Technology
Developmental biology
E-mail: kuochuwon@gmail.com
趙千嫣 (Chien-Yen Chao)
Major Fields in BS: Computer Science and Information Engineering
E-mail: sarah61633@gmail.com

Undergraduate Students

林靖智 (Jing-Zhi Lin, Chinz)
Major Fields in BS: Biological Technology        
E-mail: acps91012@gmail.com
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Alumni

Ph.D. (Total: 13)

Name Major Fields in BS Memo (Research Groups, Research Directions, Publications)
林峻宇
(Chun-Yu Lin)
Biological Technology July 2014, Ph.D.
Systems Biology: Protein-protein interaction
Journal paper: 7 papers
Current Position: Post doctor in BioXGEM
林志達
(Chih-Ta Lin)
Biological Technology July 2014, Ph.D.
Anticancer drug: Kinase-specific inhibitors & networks
Journal paper: 5 papers
Current Position: Post doctor in BioXGEM
邱一原
(Yi-Yuan Chiu)
Computer Science July 2014, Ph.D.
Computer-aided drug design
Journal paper: 4 papers
Current Position: TSMC (台積電)
陳世勳
(Shih-Hsun Chen)
Biochemical Engineering December 2013, Ph.D.
Computer-aided drug design
Journal paper: 3 papers
劉怡馨
(I-Hsin Liu)
Life Science July 2013, Ph.D.
Systems Biology: Protein-MHC-TCR interaction
Journal paper: 3 papers
羅宇書
(Yu-Shu Lo)
Life Science July 2012, Ph.D.
Systems Biology: Protein-protein interaction
Journal paper: 10 papers
Current Position: Meribank (宣捷生技)
許凱程
(Kai-Cheng Hsu)
Biological Technology July 2011, Ph.D.
Computer-aided drug design
Journal paper: 16 papers
Current Position: Taipei Medical University (臺北醫學大學)
陳彥甫
(Yen-Fu Chen)
Applied Chemistry July 2010, Ph.D.
Computer-aided drug design
Journal paper: 6 papers
(Win the 2007 National Innovation Award)
Current Position: CMC (中環科技)
黃章維
(Jhang-Wei Huang)
Biological Technology September 2010, Ph.D.
Influenza Virus: Antigenic Drift Analysis, Antigen-Antibody interaction
Journal paper: 4 papers
Current Position: CrackerBio (奎克生技光電)
陳俊辰
(Chun-Chen Chen)
Biological Technology June 2009, Ph.D.
Systems Biology: Protein-protein interaction
Journal paper: 3 papers
Current Position: 康健雜誌
董其樺
(Chi-Hua Tung)
Biological Science June 2009, Ph.D.
Structural Bioinformatics: 3D-BLAST, Antigen-Antibody interaction
Journal paper: 3 papers
Current Position: Assistant Professor, Department of Bioinformatics, Chung Hua University (中華大學)
張耀霖
(Yao-Lin Chang)
Computer Science June 2008, Ph.D.
Title: A 3D-regulog approach to predict protein-DNA binding partners and binding model
(Co-advised student with Cheng-Yan Kao in NTU)
通過高考三級資訊處理職系資訊處理類科
朱彥煒
(Yen-Wei Chu)
Computer Science June 2006, Ph.D.
Title: Finding Protein Secondary Structure Regularity and Related Applications
(Co-advised student with Chuen-Tsai Sun in NCTU)
Current Position: Associate Professor, Institute of Bioinformatics, National Chung Hsing University (中興大學)
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MD. Ph.D.

Name Major Fields in BS Memo (Research Groups, Research Directions, Publications)               
李日清
(Jih-Chin Lee)
Institute of Medical Sciences, The National Defense Medical Center July 2016, MD. Ph.D.
Journal paper: 41 papers

Master

Name Major Fields in BS Memo (Research Groups, Research Directions, Publications)
許元綸
(Yuan-Luen Sheu)
Information Management July 2016, Master
Systems Biology: Protein-protein interaction
顏佳儀
(Chia-Yi Yen)
Biological Technology July 2016, Master
Computer-aided drug design
楊方琪
(Yi-Jyun Jhen)
Biological Technology July 2016, Master
Systems Biology: Protein-protein interaction
李哲勳
(Jhuan-Dong Lin)
Biological Technology July 2016, Master
Computer-aided drug design
莊佾軒
(Yi-Shen Chung)
Computer Science July 2015, Master
Systems Biology: Protein-protein interaction
沈培鈞
(Pei-Jyun Chen)
Life Science July 2015, Master
Computer-aided drug design
陳怡君
(Yi-Jyun Jhen)
Information Management July 2015, Master
Systems Biology: Protein-protein interaction
林傳東
(Jhuan-Dong Lin)
Earth Sciences July 2015, Master
Computer-aided drug design
曾仁琥
(Jen-Hu Tseng)
Pharmacy July 2015, Master
Computer-aided drug design
林昱葦
(Yu-Wei Lin)
Biochemical Technology July 2014, Master
Systems Biology: Protein-Protein interaction
劉冠秀
(Kuan-Shiu Liu)
Computer Science July 2014, Master
Computer-aided drug design
李采凌
(Tsai-Ling Lee)
Computer Science July 2013, Master
Systems Biology: Protein-protein interaction
Journal paper: 1 paper
徐瑋澤
(Wei-Ze Syu)
Life Science July 2013, Master
Computer-aided drug design
尤宣人
(Syuan-Ren You)
Computer Science July 2012, Master
Computer-aided drug design
游宇震
(Yu-Chen, Yu)
Management Information System July 2012, Master
Systems Biology: Protein-protein interaction
李淩婷
(Ling-Ting Li)
Medicine Management July 2012, Master
Computer-aided drug design
Title: Core site-moiety maps of histone demethylase family for multi-target inhibitors and binding mechanisms
Journal paper: 3 papers
林伸融
(Shen-Rong Lin)
Computer Science July 2014, Master
Computer-aided drug design
Title: iGemdock 2.0 and SiMMap: Post-screening analysis for structure-based drug design
Journal paper: 4 paper
黃御哲
(Yu-Chi Huang)
Biological Technology July 2011, Master
Computer-aided drug design
Title: A web server for lead optimization using site-moiety map: A case study on neuraminidase
Journal paper: 1 paper
林怡瑋
(Yi-Wei Lin)
Life Science July 2011, Master
Systems Biology: Protein-protein interaction
Title: Template-based Homologous Modules through Protein-protein Interaction Families
Journal paper: 2 papers
許彥超
(Yen-Chao Hsu)
Computer Science December 2011, Master
Computer-aided drug design
Title: Moiety-based site-moiety map
林韋帆
(Wei-Fan Lin)
Life Science July 2011, Master
Influenza Virus: Antigenic Drift Analysis
Title: Genetic and antigenic analysis to the hemagglutinin of influenza A H1N1 virus and comparisons with H3N2 virusJournal paper: 1 paper
張力仁
(Li-Jen Chang)
Life Science July 2010, Master
Structural Bioinformatics
林峻宇
(Chun-Yu Lin)
Biological Technology May 2010, Master
Systems Biology: Protein-protein interaction
Journal paper: 2 papers
陳彥修
(Yen-Hsiu Chen)
Life Science June 2009, Master
Systems Biology: Protein-DNA/Protein-RNA interaction
劉康平
(Kang-Ping Liu)
Computer Science June 2009, Master
Systems Biology: Protein-protein interaction
Journal paper: 1 paper
陳祐德
(Yu-Te Chen)
Aquaculture June 2008, Master
Title: A New Profile Method to Predict Protein-ligand Binding Site
羅宇書
(Yu-Shu Lo)
Life Science June 2008, Master
Title: Template-Based Scoring Function for Predicting Protein-protein Interaction
Journal paper: 2 papers
許凱程
(Kai-Cheng Hsu)
Biological Technology June 2007, Master
Title: Binding Affinity Analysis of Protein-ligand Complexes
陳右儒
(Yo-Ru Chen)
Computer Science June 2007, Master
Title: iGEMDOCK: A graphical-automatic drug design system for docking, screening and post-analysis
(Win the 2007 National Innovation Award)
Current Position: MediaTek (聯發科)
楊登凱
(Teng-Kai Yang)
Computer Science June 2006, Master
Title: Structural Binding Pocket Clustering and Protein-ligand Interaction Analysis for ATP-binding Proteins
陳永強
(Yung-Chiang Chen)
Life Science June 2006, Master
Title: Inferring Domain Annotated Protein-Protein Interactions through 3D-Domain Interologs
Journal paper: 2 papers
葛振寧
(Chen-Neng Ko)
Biological Science June 2006, Master
Title: Structure-based Compound Screening for Helicobacter pylori shikimate kinase (HpSK)
Journal paper: 1 paper
黃章維
(Jhang-Wei Huang)
Biological Technology June 2006, Master
Title: Predicting Antigenic Variants of Influenza A H3N2 Viruses by Building Relationships between Genetic Evolution and Antigenic Drift
Journal paper: 2 papers
董其樺
(Chi-Hua Tung)
Biological Science June 2005, Master
Title: PiSA-BLAST: A New Tool for Protein Structure Alignment and Database Search
(Win the prize of 2005 Best M.S. and Ph. D. Dissertation Award hosted by IICM (Institute of Information & Computing Machinery))
Website: 3D-BLAST
Journal paper: 3 papers
邱一原
(Yi-Yuan Chiu)
Computer Science June 2005, Master
Title: Optimizing New Energy Functions for Protein Folding
Journal paper: 1 paper
林柏村
(Po-Tsun Lin)
Life Science June 2005, Master
Title: LigSeeSVM: Support Vector Machines and Data fusion for Ligand-based Compound Screening and Applications to GPCR and GABAA
陳宏助
(Heng-Chu Chen)
Life Science June 2005, Master
Title: Inferring Protein-protein Interactions from Structural Domain-domain Interactions
張立人
(Li-Jen Chang)
Medical Technology June 2005, Master
Title: Integrating GEMDOCK with GEM-PLS and GEM-kNN for QSAR modeling of huAChE and AGHO
沈再威
(Tsai-Wei Shen)
Biological Science June 2004, Master
Title: Enhancing GEMDOCK on Virtual Database Screening and Application to Envelope Protein and D-Hydantoinase
(Win the prize of 2004 Best M.S. and Ph. D. Dissertation Award hosted by IICM (Institute of Information & Computing Machinery))
Website: GEMDOCK
Journal paper: 2 papers
林建宏
(Chien-Heng Lin)
Biological Science June 2004, Master
Title: MuLiSA: Analysis and Identification of Functional Motifs and Residues in Proteins by Multiple Ligand-bound Structure Alignments
陳彥甫
(Yen-Fu Chen)
Applied Chemistry June 2004, Master
Title: Validation and Application of GEMDOCK and Application of Data Fusion in Virtual Screening
Journal paper: 2 papers
張育祥
(Yu-Hsiang Chang)
Life Science June 2003, Master
Title: A New Energy Model for Protein-Protein Interaction Prediction
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建立藥物-蛋白質-生化途徑-疾病機制的關連

建立基礎研究-轉譯醫學-產業的連結

Overview

    Our research focused on computer-aided drug design (GEMDOCK and SiMMap), structural bioinformatics (3D-BLAST, (PS)2 and fastSCOP), and systems biology (PPISearch and 3D-partner), especially investigating the molecular interfaces (e.g., protein-protein, protein-DNA, protein-ligand interactions). Our main contributions and innovations are described as follows: I) Discover the protein-compound interaction family for multi-target drug design and new uses for old drug [1-4]. II) The first team proposed protein-protein interactions (interface family) across multiple species [5-8]. III) We have developed the first tool, called 3D-BLAST which is as fast as BLAST and has the features of BLAST (e.g. robust statistical basis, and effective and reliable search capabilities), to search large protein structures (> 30000) within 3 seconds in the world [9-11].

Drug discovery: Pharmalogs and Homopharma

    For structure-based protein-ligand interactions and drug discovery, we have developed a molecular docking tool, namely GEMDOCK [3, 4, 13, 14], which is one of wide-used tools in the world. We cooperated with 10 research teams on diverse drug targets. We cooperated with over 10 laboratories which successfully applied our tools for identifying lead compounds and protein functional sites and protein engineering. For example, GEMDOCK has been successfully applied to identify the lead compounds for dengue virus envelop protein (cooperating with Yang YL in NCTU)[2]; inhibitors of influenza virus neuraminidase (cooperating with Hsu TA in NHRI) [15]; lead compounds of ROCK kinase (cooperating with Chao JI in NCTU) for anti-cancer drugs; antibiotics of shikimate kinases of Mycobacterium tuberculosis and Helicobacter pylori (cooperating with Wang WC in NTHU). We have successfully applied our tools for discovering the secondary vitamin D3 binding site of milk beta-lactoglobulin (cooperating with Mao JI in NCTU)[16, 17]; the binding mechanism between c-di-GMP ad cAMP Receptor-Like Protein CLP (cooperating with Chao SH in NCHU) [18]. The timed citations of two related papers [3, 13] are 58 and 61, respectively, from 2004. These related papers were cited over 180 times. We got the 2007 National Innovation Award due to the achievement of iGEMDOCK.
    在藥物開發部份,本實驗室透過獨立研發的全台第一個藥物嵌合軟體 GEMDOCK(榮獲 2007 國家新創獎)與超過 400 個 CPU 的計算資源,可快速的針對特定藥物標靶於虛擬藥物資料庫中(超過 30 萬筆小分子化合物)進行篩選,並利用全球首創的區域官能基地圖技術分析標靶蛋白的藥物結合機制,進而篩選出新型抑制劑。有別於其他計算實驗室缺乏自主實驗驗證,我們已建構由全波長式多功能微量分析儀暨冷螢光數位影像分析系統為主的高效藥篩平台,可對篩選出的抑制劑進行活性分析,並可針對常見癌症(肝癌、乳癌、頭頸癌)或發炎反應進行細胞實驗分析。此外,我們並與淡水馬偕醫院與三軍總醫院合作進行臨床試驗,是國內少數從計算跨足轉譯醫學的藥物設計與系統生物實驗室。在癌症與許多複雜疾病的主要藥物標靶-蛋白激酶上,我們透過上述程序,發現了特定受體酪氨酸激酶專屬的結合位點(Type-C pocket),並成功針對此位點篩選出選擇性抑制劑(Type-C inhibitors),而大規模蛋白激酶抑制活性分析結果亦顯示出高選擇性,並能克服傳統化療藥物所產生的常見抗藥性突變,順利突破此類年產值高達 185 億美金的藥物目前所面對的瓶頸--選擇性與抗藥性,為其選擇性與抗藥性設計開闢另一個方向。

Molecular interface families (protein-drug, protein-protein, and protein-DNA)

    In protein-peptide interactions, we improved our PPI template-based scoring function with template similarity and interacting force to guarantee statistically significant interface similarity between peptide candidates and structure templates. Our model, considering both MHC-peptide and peptide-TCR interfaces, could provide visualization and biological insights of MHC-peptide-TCR binding models. We believe that it is very helpful for the development of peptide-based vaccines. For protein-DNA interactions, we developed a new approach, namely 3D-regulogs, to infer protein-DNA binding partners by using the concept of regulog and crystal structures of protein-DNA complex as templates [12]. This approach also provides binding models, interacting amino acids, and DNA bases of predicted partners. For protein-ligand interactions, we have introduced site-moiety maps [1], which recognize interaction preferences between protein pockets and compound moieties. SiMMap was developed to identify site-moiety maps from query protein structures and their docked (or co-crystallized) compounds. Over 1,400 users have created more than 1,500 site-moiety maps for different proteins. Site-moiety map is able to provide biological insights and useful for drug discovery and lead optimization.

Homologous structural systems biology

    For systems biology and structural bioinformatics, we have proposed a novel concept, called "3D-domain interologs", to discover protein-protein interactions[6-8] and protein-DNA interactions [12] which are considered as orthologous interactions among different species, in particular about inferred interacting domain pairs and binding models (e.g. hydrogen-bond interactions and conserved residues). For protein-protein interactions, we proposed the PPISearch server [5] for searching homologous protein-protein interactions (PPIs), called PPI family, across multiple species. According to our knowledge, PPISearch is the first public server that identifies homologous PPIs from annotated PPI databases and infers transferability of interacting domains and functions between homologous PPIs and the query. By taking account of structural bioinformatics cross species, we extended PPISearch to PCFamily [8], which is useful for binding model visualizations and annotating query proteins based on homologous protein complexes. Until September 2010, over 3,500 users have used PPISearch and PCFamily servers. Furthermore, the number of accessing 3D-BLAST exceeds 6,000 from 44 countries and related papers were cited ~50 times since 2007.

藥物傳輸老藥新用:尼古丁乙醯膽鹼受體α9在尼古丁誘導之癌症中的調控機制

    本團隊與台北醫學大學乳癌研究團隊(何元順教授團隊及雙和醫院院長 吳志雄教授等)合作,探討尼古丁(Nicotine)誘導多種疾病(如肺癌、頭頸癌、乳癌、畸形兒等)發生之轉譯醫學研究,尼古丁乙醯膽鹼受體α9(α9-nAChR)被認為參與由尼古丁所誘發的人類正常乳腺上皮細胞的轉型,由於目前所有的PPI資料庫都缺乏α9-nAChR的交互作用蛋白質,我們透過同源映射網路及蛋白質-化合物交互作用家族概念,發現5個新的α9-nAChR之交互作用蛋白質(X1、X2、X3、X4和X5)及其相關生化途徑。透過免疫共沉澱及螢光共振能量轉移影像(Förster resonance energy transfer),發現α9-nAChR正常情況下會與生長因子受體(如X1、X2)結合,降低其活性;當尼古丁結合α9-nAChR會使其與生長因子受體分離,因而活化下游生化途徑抑制細胞凋亡及促進細胞增生。目前已將此發現透過臨床檢體進行驗證,成功發現尼古丁誘發乳癌之機制,相關成果發表撰寫中。

天然藥新藥開發

    中草藥在中華民族的生活與歷史上扮演重要角色,然而隨著西風東漸,國人因為中草藥的傳統理論基礎缺乏現今科學化的解釋而漸趨勢微,這無論對已有數千年臨床驗證的中草藥或是對人類的健康都是一大損失,所以將中草藥的療效賦予科學化的解釋是相當重要且刻不容緩的。本實驗室透過系統生物的策略,建構出跨物種的同源交互作用網絡,並成功解釋疾病的致病機制。並透過在藥物設計領域的積累,提出全球首創的同源藥理概念,可利用蛋白與藥物的共結晶結構預測出其他具有類似結合機制的標靶蛋白與藥物,有助於舊藥新用與副作用預測。而本實驗室進一步將系統生物與藥物設計結合,可透過將中草藥或整株植物的成分以同源藥理概念找出潛在作用蛋白,並標註於同源交互作用網絡,如此將可以作用標靶、作用途徑、影響疾病等科學化方式闡述中草藥的療效,目前並已成功應用於痲瘋樹、紅麴與牛樟芝的治療與保健功效預測上。

抗癌與抗感染藥物開發:頭頸癌病人傳統藥物治療偕同健康食品進行輔助療法

    本團隊與三軍總醫院頭頸癌研究團隊(病理部聶鑫主任及李日清醫師)合作,透過系統生物策略模型,發展可以用於診斷、預後及治療之頭頸癌生物標記-HNC88(88個基因),並試圖以 HNC88 從分子階層角度對病患進行分類與治療,大致可將病患分成 HPV-infected、Immune-enriched 及 Proliferation-enriched 三大類。葡萄王生技為國內保健食品製造龍頭,本團隊與葡萄王生技合作進行生技健康食品科學化及功效驗證,如:分析樟芝王關鍵成分對口腔癌病患化放療之副作用緩解分析及預後評估,探討食用前、後之各病患子類血液中基因表現與癌症生化途徑的變化。

腦及神經老化藥物開發

    人類對於大腦運作所負責的腦區已有了解但對於詳細運作機制仍然尚未釐清,因此對於大腦研究進而衍伸出幾個議題:1. 因應世界人口老齡化的趨勢因而衍生出老年神經退化性疾病,例如:阿茲海默症,根據統計在 2010 年全球有將近 2100 萬到 3500 萬名阿茲海默症患者,而歸因於阿茲海默症相關的死亡案例大約有 48.6 萬例。阿茲海默症會使患者越來越需要他人的照護,因此導致在已開發國家中阿茲海默症是相當耗費社會資源的疾病之一。世界衛生組織指出目前並沒有特定藥物有實證證明對阿茲海默症治療有效,只有少數可能可以暫時(緩解)改善症狀的方法,而健康食品及植物藥被視為是另類可能的有效途徑;2. 由於許多大腦疾病已知與性別有關,例如:男生易患自閉症、女生易患阿茲海默症,因此透過了解男女大腦先天上的差異對於釐清疾病病理機制具有莫大幫助,本團隊透過表徵型資料:腦電波圖譜(EEG)、大腦核磁共振(MRI)、動物模式,以及基因型資料:基因表達圖譜(mRNA microarray)、次世代定序(NGS)、蛋白質體圖譜(Proteomics),整合本團隊核心技術蛋白質交互作用家族(PPI family)、模組交互作用家族(Module family)、蛋白質-配體交互作用家族(Protein-ligand family),進而揭露大腦疾病詳細生化機制。

合作夥伴

    We have accumulated extensive experiences in drug design to achieve the specific aims. Our team consists of experts in different fields, including computational drug design, systems biology, clinical trial, lead optimization, biochemistry, and animal models. We have successfully discovered 45 lead compounds (<10 μM) for various diseases or pathogens. One of the identified natural compounds, rosmarinic acid, is currently applying for the U.S. patent and IRB approval at Mackay Memorial Hospital (馬偕醫院) for clinical trials. Based on these results, we have received one U.S. patent (US 8,175,860 B2), and have applied one U.S. patent (13/872,456) and one ROC patent. In university-industry collaborations, we have collaborated with ScinoPharm (台灣神隆), Phalanx Biotech Group (華聯生技), Food Industry Research and Development Institute (食品工業研究所), and Jason Life Tech for developing new drugs, botanical drugs, healthy food, and microarray platform for detecting diseases. We have collaborated with over 30 laboratories (e.g., Professor Wang HJ [王惠鈞院士] and Professor Mark von Itzstein, inventor of the first anti-influenza drug, Zanamivir), five teaching hospitals, and 15 national institutes for drug discovery, systems biology, binding mechanisms, and multi-target drugs. In addition, we have achieved some significant results in molecular interactions and structural systems biology: 1) We are the first team proposed molecular-interface families; 2) We have established the statistical biophysics methods to infer site-moiety maps (hotspots) of proteins for protein-ligand binding mechanisms and drug discovery; 3) We have proposed the comprehensive molecular interaction networks for studying interactomes; 4) We have developed GEMDOCK, which is a world-wide used docking programs.

References

  1. Chen YF, Hsu KC, Lin SR, Wang WC, Huang YC, Yang JM: SiMMap: a web server for inferring site-moiety map to recognize interaction preferences between protein pockets and compound moieties. Nucleic Acids Research 2010, 38:W424-W430.
  2. Yang JM, Chen YF, Tu YY, Yen KR, Yang YL: Combinatorial computational approaches to identify tetracycline derivatives as flavivirus inhibitors. PLoS ONE 2007:e428.
  3. Yang JM, Chen CC: GEMDOCK: a generic evolutionary method for molecular docking. Proteins: Structure, Function, and Bioinformatics 2004, 55:288-304.
  4. Yang JM, Shen TW: A pharmacophore-based evolutionary approach for screening selective estrogen receptor modulators. Proteins: Structure, Function, and Bioinformatics 2005, 59:205-220.
  5. Chen CC, Lin CY, Lo YS, Yang JM: PPISearch: a web server for searching homologous protein-protein interactions across multiple species. Nucleic Acids Research 2009, 37:W369-W375.
  6. Chen YC, Lo YS, Hsu WC, Yang JM: 3D-partner: a web server to infer interacting partners and binding models. Nucleic Acids Research 2007:W561-W567.
  7. Lo YS, Chen YC, Yang JM: 3D-interologs: An evolution database of physical protein-protein interactions across multiple genomes. BMC Genomics 2010, 11, Suppl 3:S7.
  8. Lo YS, Lin CY, Yang JM: PCFamily: a web server for searching homologous protein complexes. Nucleic Acids Research 2010, 38:W516-W522.
  9. Yang JM, Tung CH: Protein structure database search and evolutionary classification. Nucleic Acids Research 2006, 34:3646-3659.
  10. Tung CH, Huang JW, Yang JM: Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database. Genome Biology 2010, 2007, 8:R31.
  11. Tung CH, Yang JM: fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies. Nucleic Acids Research 2007, 35:W438-W443.
  12. Chang YL, Tsai HK, Kao CY, Chen YC, Hu YJ, Yang JM: Evolutionary conservation of DNA-contact residues in DNA-binding domains. BMC Bioinformatics 2008, 9(S6):S3.1-S3.9.
  13. Yang JM, Chen YF, Shen TW, Kristal BS, Hsu DF: Consensus scoring criteria for improving enrichment in virtual screening. Journal of Chemical Information and Modeling 2005, 45:1134-1146.
  14. Yang JM: Development and evaluation of a generic evolutionary method for protein-ligand docking. Journal of Computational Chemistry 2004, 25:843-857.
  15. Hung HC, Tseng CP, Yang JM, Ju YW, Tseng SN, Chen YF, Chao YS, Hsieh HP, Shih SR, Hsu JT: Aurintricarboxylic acid inhibits influenza virus neuraminidase. Antiviral Research 2009, 81:123-131.
  16. Yang MC, Guan HH, Liu MY, Lin YH, Yang JM, Chen WL, Chen CJ, Mao SJT: Crystal Structure of a Secondary Vitamin D3 Binding Site of Milk ß-Lactoglobulin. Proteins: Structure, Function, and Bioinformatics 2008:1197-1210.
  17. Yang MC, Guan HH, Yang JM, Ko CN, Liu MY, Lin YH, Chen CJ, Mao SJT: Rational Design for crystallization of b-Lactoglobulin and vitamin D3 complex: reveal of a secondary binding site. Crystal Growth & Design 2008:DOI: 10.1021/cg800697s.
  18. Chin KH, Lee YC, Tu ZL, Chen CH, Tseng YH, Yang JM, Ryan RP, McCarthy Y, Dow JM, Wang AH et al: The cAMP receptor-like protein CLP is a novel c-di-GMP receptor linking cell-cell signaling to virulence gene expression in Xanthomonas campestris. Journal of Molecular Biology 2010, 396:646-662.

BioXGEM 所發展的生物資訊網頁工具及資料庫

GEMDOCK

GEMDOCK - a Generic Evolutionary Method for molecular DOCKing GEMDOCK is a program for computing a ligand conformation and orientation relative to the active site of target protein. The tool was developed by Jinn-Moon Yang, a profesor of the Institute of Bioinformatics, National Chiao Tung University.
URL: http://gemdock.life.nctu.edu.tw/dock/


SiMMap

SiMMap: Site-moiety map for drug discovery and mechanisms
URL: http://simmap.life.nctu.edu.tw/


3D-BLAST

3D-BLAST is a very fast and accurate method for discovering the homologous proteins and evolutionary classifications of a newly determined protein structure. Our 3D-BLAST has the advantages of BLAST tool for fast protein structure database scanning.
URL: http://3d-blast.life.nctu.edu.tw/


Protein-Protein Interaction Search

Input an interacting protein pair as a query to search its homologous interactions across multiple species
URL: http://140.113.15.76/ppisearch/


PCFamily

PCFamily : Protein Complex Family Search
URL: http://pcfamily.life.nctu.edu.tw/


MoNetFamily

MoNetFamily - Homologous modules and module-module interaction networks in vertebrates
URL: http://monetfamily.life.nctu.edu.tw/index.php


KIDFamMap

KIDFamMap: Kinase-inhibitor-disease family map
URL: http://gemdock.life.nctu.edu.tw/KIDFamMap/


歡迎有熱情 有想法的碩博生 專題生加入我們的行列
誠徵博士後研究員 碩士級專任研究助理
THE WORLD OF DRUG DISCOVERY,
FUNCTION BIOINFORMATICS AND SYSTEMS BIOLOGY.





楊進木 教授
03-5712121 #56942 (Lab: #56946)
moon@faculty.nctu.edu.tw
生科實驗館 308 室
研究內容
  • 生物領域
    • 藥物設計、系統生物與結構生物學
    • 成功對 15 個標靶蛋白質發現 43 個前導藥物,如肺癌、前列腺癌、結核桿菌、幽門螺旋桿菌、流感病毒
    • 全球第一建立蛋白質-蛋白質交互作用家族與跨多物種模組-模組交互作用網路

發現四環抗生素對
登革熱病毒有效

  • 資訊領域
    • 軟體撰寫、網頁與資料庫設計
    • 開發了 9 個生物技術產業及新藥開發的網頁服務或工具
    • GEMDOCK 獲得 2007 國家新創獎
    • 3D-BLAST 為目前最快的蛋白質結構搜尋工具
  • 拓展視野
    • 與第一個抗流感藥物發明者(Mark von Itzstein)、藥華藥廠、4 個教學醫院和 12 個國家型機構合作(如中研院與國衛院)
  • 就業發展
    • 生技產業、資訊科技業、研究人員、教職

活動照片

運動

時間 ► 2015年5月7日 (星期四)
地點 ► 國立交通大學光復校區 排球場

參加生科系運排球比賽賽後合照

出遊

時間 ► 2014年2月18日 (星期二)
地點 ► 老師的農莊

在老師的農莊摘橘子

耶誕晚會

時間 ► 2013年12月23日 (星期一)
地點 ► 國立交通大學博愛校區 生科實驗館 生資中心

耶誕晚會交換禮物

謝師宴

時間 ► 2013年8月7日 (星期三)
地點 ► 新竹加賀日本料理

在加賀日本料理舉辦謝師宴

成員合照

研討會集錦