BioXGEM: 藥物設計與系統生物實驗室

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Achievement

According to Essential Science Indicators (ESI), I have three highly cited papers

Published over 100 papers and I am the corresponding authors for some top journals as follows:
(1) Genome Biology (IF=18.011)
(2) 10 papers in Nucleic Acids Research (IF=19.16)
(3) Nature Communications (IF=17.694)
(4) ACS Nano (IF=18.027)
(5) Clinical Infectious Diseases (IF=20.999)

We have over 10 patents and discovered more than 30 lead drugs

My h-index is 36 and the number of citations is over 5,300 ( Google scholar )

Our main research works and achievements can be briefly summarized as follows:

We published Taiwan's first molecular docking paper in top-rank journal and developed it as iGEMDOCK (BMC Bioinformatics, selected as highly cited paper ), which is one of widely used docking tools in the world. iGEMDOCK has been downloaded more than 100,000 times and has won the National Innovation Award. Furthermore, aiming to solve the low accuracy of virtual drug screening, we have proposed homopharma (protein-ligand interface family) and SiMMap to greatly improve the accuracy, hit rate of drug discovery, and for investigating drug binding and inhibition mechanisms supported by experimental verification. These results have been published in Genome Biology and Nucleic Acids Research , and we have obtained a US patent.

In computational systems biology, we pioneered innovative theories and tools of protein-protein interaction family and protein module family, and published five papers in Nucleic Acids Research . Through interdisciplinary cooperation and experimental validation, we have successfully discovered biomarkers and identified disease subtypes for the diagnosis and treatment of several cancers (e.g., head and neck cancer and triple-negative breast cancer). Some of these results have been published in Nature Communications (2019) and Cancers (2020).

For cancer precision medicine, we established Cancer Membrane Protein-regulated Networks (CaMPNets) comprising of nearly 2,000 membrane proteins (MP) in 15 diverse cancers to explore their roles in cancers, and then applied CaMPNets to clinical prognostic biomarkers identification and drug development. The cell and animal results validated our models, discovered the target MP and its FDA drug in triple-negative breast cancer. These results were published in Nature Communications (2019) and we obtained two ROC patents (2021) and filed a U.S. patent application.

For COVID-19 drug repurposing, we have integrated pharmacophore-based models and site-moiety maps to uncover flexible active site conformations of SARS-CoV-2 3CL Proteases. Our model discovered Boceprevir (IC50=1.42 μM and EC50=49.89 μM) and Telaprevir (both HCV drugs) and Nelfinavir (HIV drug) as potential COVID-19 drugs ( ACS Nano , 2021). Furthermore, we have developed a NetPharma framework, combining homopharma and evolution-based systems biology, to discover a multi-target FDA drug (JMY206, better than Remdesivir) of COVID-19. JMY206 in infected hamster model (validation by Taiwan's only P4 laboratory, National Defense Medical Center) can prevent lung damage and inflammation by modulating neutrophil infiltration and innate/ adaptive immune responses. Based on these results, we prepared papers for publication, applied two U.S. provisional patent applications (ID: 63160507 and 63160518) and clinical applications.

Huang, H. L., Lee, J. Y., Lo, Y. S., Liu, I. H., Huang, S. H., Huang, Y. W., Lee, M. R., Lee, C. H., Cheng, M. H., Lu, P. L., Wang, J. Y.*, Yang, J. M.* , Chong, I.W. (2022) Whole-blood 3-gene signature as a decision sid for rifapentine-based TB preventive therapy , Clinical Infectious Diseases , doi: 10.1093/cid/ciac003. (IF=20.999) Huang, Y. W., Hsu, Y. C., Chuang, Y. H., Chen, Y. T., Lin, X. Y., Fan, Y. W., Pathak, N., Yang, J. M.* (2022) Discovery of moiety preference by Shapley value in protein kinase family using random forest models , BMC Bioinformatics , 23, doi: 10.1186/s12859-022-04663-5. Pathak, N., Chen, Y. T., Hsu, Y. C., Hsu, N. Y., Kuo, C. J., Tsai, H. P., Kang, J. J., Huang, C. H., Chang, S. Y., Chang, Y. H., Liang, P. H. and Yang, J. M.* (2020) Uncovering Flexible Active Site Conformations of SARS-CoV-2 3CL Proteases through Protease Pharmacophore Clusters and COVID-19 Drug Repurposing , ACS nano , 15(1), 857-872, doi: 10.1021/acsnano.0c07383. Chuang, Y. H., Huang, S. H., Hung, T. M., Lin, X. Y., Lee, J. Y., Lai, W. S. and Yang, J. M.* (2021) Convolutional neural network for human cancer types prediction by integrating protein interaction networks and omics data , Scientific Reports , 11:20691. Lin, C. Y., Lee, C. H., Chuang, Y. H., Lee, J. Y., Chiu, Y. Y., Lee, Y. H. W., Jong, Y. J., Hwang, J. K., Huang, S. H., Chen, L. C., Wu, C. H., Tu, S. H., Ho, Y. S., Yang, J. M.* (2019) Membrane protein-regulated networks across human cancers , Nature Communications , 10(1):3131. 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 , 41(Database issue):D430-40. 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(7):e1003127. 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(Web Server issue):W263-70. 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 , 57(14):5975-85. 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. 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(3):R31. 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(Web Server issue):W561-7. Chen, C. C., Hwang, J. K., and Yang, J. M.* (2006) (PS)(2): protein structure prediction server , Nucleic Acids Research , 34(Web Server issue):W152–7. 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(4):1134-46. Yang, J. M.* , and Chen, C. C. (2004) GEMDOCK: A generic evolutionary method for molecular docking , Proteins-Structure Function and Bioinformatics , 55(2):288-304.

Complete Journal Papers

Chen, Y. T., Li, J., Chang, J. N., Luo, Y. C., Yu, W., Chen, L. C. and Yang, J. M.* (2023) Transcriptomic analysis of World Trade Center particulate Matter-induced pulmonary inflammation and drug treatments , Environment International 108027. Chen, Y. T., Chang, Y. H., Pathak, N., Tzou, S. C., Luo, Y. C., Hsu, Y. C., Li, T. N., Lee, J. Y., Chen, Y. C., Huang, Y. W., Yang, H. J., Hsu, N. Y., Tsai, H. P., Chang, T. Y., Hsu, S. C., Liu, P. C., Chin, Y. F., Lin, W. C., Yang, C. M., Wu, H. L., Lee, C. Y., Hsu, H. L., Liu, Y. C., Chu, J. W., Wang, L. H. C., Wang, J. Y., Huang, C. H., Lin, C. H., Hsieh, P. S., Wu Lee, Y. H., Hung, Y. J. and Yang, J. M.* (2022) Methotrexate inhibition of SARS-CoV-2 entry, infection and inflammation revealed by bioinformatics approach and a hamster model , Frontiers in Immunology 13: 7590. Huang, H. C., Chen, Y. T., Lin, H. H., Li, Z. Q., Yang, J. M. and Tzou, S. C. (2022) Inhibition of IRAK1 Is an Effective Therapy for Autoimmune Hypophysitis in Mice , International Journal of Molecular Sciences 23.23: 14958. Li, R., Lee, J. Y., Yang, J. M. and Akutsu, T. (2022) Densest subgraph-based methods for protein-protein interaction hot spot prediction , BMC Bioinformatics 23.1: 1-12. Li, L. Y. J., Wang, S. Yi., Yang, J. M. , Chen, C. J., Tsai, C. Y., Wu, L. Y. Y., Wu, T. F., Wu, C. J. (2022) The Development and Evaluation of a Smartphone-Aided Diagnosis Application to Measure Tympanic Membrane Perforations , Ear, Nose & Throat Journal , 01455613221123361. Fan, Y. W., Liu, W. H., Chen, Y. T., Hsu, Y. C., Pathak, N., Huang, Y. W., and Yang, J. M.* (2022) Exploring kinase family inhibitors and their moiety preferences using deep SHapley additive exPlanations , BMC Bioinformatics , 23(4), 1-18. Lin, X. Y., Huang, Y. W., Fan, Y. W., Chen, Y. T., Pathak, N., Hsu, Y. C. and Yang, J. M.* (2022) Identification of pan-kinase-family inhibitors using graph convolutional networks to reveal family-sensitive pre-moieties , BMC Bioinformatics , 23(4), 1-13. Huang, Y. W., Hsu, Y. C., Chuang, Y. H., Chen, Y. T., Lin, X. Y., Fan, Y. W., Pathak, N. and Yang, J. M.* (2022) Discovery of moiety preference by Shapley value in protein kinase family using random forest models , BMC Bioinformatics , 23(4), 1-14. Wang, F., Chen, Y. T., Yang, J. M. and Akutsu, T. (2022) A novel graph convolutional neural network for predicting interaction sites on protein kinase inhibitors in phosphorylation , Scientific Reports , 12:229. Huang, H. L., Lee, J. Y., Lo, Y. S., Liu, I. H., Huang, S. H., Huang, Y. W., Lee, M. R., Lee, C. H., Cheng, M. H., Lu, P. L., Wang, J. Y., Yang, J. M. and Chong, I. W. (2022) Whole-blood 3-gene Signature as a Decision Aid for Rifapentine-based TB Preventive Therapy , Clinical Infectious Diseases . Chuang, Y. H., Huang, S. H., Hung, T. M., Lin, X. Y., Lee, J. Y., Lai, W. S. and Yang, J. M.* (2021) Convolutional neural network for human cancer types prediction by integrating protein interaction networks and omics data , Scientific Reports , 11:20691. Chiou, W. C., Hsu, M. S., Chen, Y. T., Yang, J. M. , Tsay, Y. G., Huang, H. C., and Huang, C. (2021) Repurposing existing drugs: identification of SARS-CoV-2 3C-like protease inhibitors , Journal of Enzyme Inhibition and Medicinal Chemistry , 36(1), 147-153. Chiou, W. C., Chen, J. C., Chen, Y. T., Yang, J. M. , Hwang, L. H., Lyu, Y. S., Yang, H. Y. and Huang, C. (2021) The inhibitory effects of PGG and EGCG against the SARS-CoV-2 3C-like protease , Biochemical and biophysical research communications . Pathak, N., Chen, Y. T., Hsu, Y. C., Hsu, N. Y., Kuo, C. J., Tsai, H. P., Kang, J. J., Huang, C. H., Chang, S. Y., Chang, Y. H., Liang, P. H. and Yang, J. M.* (2020) Uncovering Flexible Active Site Conformations of SARS-CoV-2 3CL Proteases through Protease Pharmacophore Clusters and COVID-19 Drug Repurposing , ACS nano , 15(1), 857-872, doi: 10.1021/acsnano.0c07383. Hsu, K. C., HuangFu, W. C., Lin, T. E., Chao, M. W., Sung, T. Y., Chen, Y. Y., Pan, S. L., Lee, J. C., Tzou, S. C., Sun, C. M. and Yang, J. M.* (2020) A site-moiety map and virtual screening approach for discovery of novel 5-LOX inhibitors , Scientific reports , 10(1), 1-12. Chuang, Y. H., Lee, C. H., Lin, C. Y., Liu, C. L., Huang, S. H., Lee, J. Y., Chiu, Y. Y., Lee, J. C., Yang, J. M.* (2020) An Integrated Genomic Strategy to Identify CHRNB4 as a Diagnostic/Prognostic Biomarker for Targeted Therapy in Head and Neck Cancer , Cancers , 12(5), 1324. Hengphasatporn, K., Plaimas, K., Suratanee, A., Wongsriphisant, P., Yang, J. M. , Shigeta, Y., Chavasiri, W., Boonyasuppayakorn, S., Rungrotmongkol, T. (2020) Target Identification Using Homopharma and Network-Based Methods for Predicting Compounds Against Dengue Virus-Infected Cells , Molecules , 25(8), 1883. Yang, W. Y., Rao, P. S., Luo, Y. C., Lin, H. K., Huang, S. H., Yang, J. M.* , Yuh, C. H.* (2019) Omics-based Investigation of Diet-induced Obesity Synergized with HBx, Src, and p53 Mutation Accelerating Hepatocarcinogenesis in Zebrafish Model , Cancers , 11(12), 1899. Simak, M., Lu, H. H. S., Yang, J. M. (2019) Boolean function network analysis of time course liver transcriptome data to reveal novel circadian transcriptional regulators in mammals , Journal of the Chinese Medical Association , 82(11), 872-880. Lin, C. Y., Lee, C. H., Chuang, Y. H., Lee, J. Y., Chiu, Y. Y., Lee, Y. H. W., Jong, Y. J., Hwang, J. K., Huang, S. H., Chen, L. C., Wu, C. H., Tu, S. H., Ho, Y. S., Yang, J. M.* (2019) Membrane protein-regulated networks across human cancers , Nature Communications , 10(1):3131. Lee, J. Y., Lin, S. Y., Lin, C. Y., Chuang, Y. H., Huang, S. H., Tseng, Y. Y., Wang, H. J., Yang, J. M.* (2019) Identification of the PCA29 gene signature as a predictor in prostate cancer , Journal of Bioinformatics and Computational Biology , 17(3):1940006. Lin, C. Y., Ruan, P. Y., Li, R. M., Yang, J. M. , See, S., Song, J. N., Akutsu, T. (2019) Deep learning with evolutionary and genomic profiles for identifying cancer subtypes , Journal of Bioinformatics and Computational Biology , 17(3):1940005. Lee, C. C., Chang, W. H., Chang, Y. S., Yang, J. M. , Chang, C. S., Hsu, K. C., Chen, Y. T., Liu, T. Y., Chen, Y. C., Lin, S. Y., Wu, Y. C., Chang, J. G. (2019) Alternative splicing in human cancer cells is modulated by the amiloride derivative 3,5-diamino-6-chloro-N-(N-(2,6-dichlorobenzoyl)carbamimidoyl)pyrazine-2-carboxide , Molecular Oncology , 13(8):1744-1762. Huang, L. C., Tam, K. W., Liu, W. N., Lin, C. Y., Hsu, K. W., Hsieh, W. S., Chi, W. M., Lee, A. W., Yang, J. M. , Lin, C. L., Lee, C. H. (2018) CRISPR/Cas9 Genome Editing of Epidermal Growth Factor Receptor Sufficiently Abolished Oncogenicity in Anaplastic Thyroid Cancer , Disease Markers , 3835783. Huang, S. H., Lo, Y. S., Luo, Y. C., Tseng, Y. Y., Yang, J. M.* (2017) A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations , BMC Systems Biology , 12(2):13. Pathak, N., Lai, M. L., Chen, W. Y., Hsieh, B. W., Yu, G. Y., Yang, J. M.* (2017) Pharmacophore anchor models of flaviviral NS3 proteases lead to drug repurposing for DENV infection , BMC Bioinformatics , 18(16):548. Lai, W. S., Cheng, S. Y., Lin, Y. Y., Yang, P. L., Lin, H. C., Cheng, L. H., Yang, J. M. , Lee, J. C. (2017) Clinical assessment of diode laser-assisted endoscopic intrasphenoidal vidian neurectomy in the treatment of refractory rhinitis , Lasers in Medical Science , 32(9):2097-104. Huang, L. C., Lin, C. L., Qiu, J. Z., Lin, C. Y., Hsu, K. W., Tam, K. W., Lee, J. Y., Yang, J. M. , Lee, C. H. (2017) Nicotinic Acetylcholine Receptor Subtype Alpha-9 Mediates Triple-Negative Breast Cancers Based on a Spontaneous Pulmonary Metastasis Mouse Model , Frontiers in Cellular Neuroscience , 11:336. Hsu, K. C., Hung, H. C., HuangFu, W. C., Sung, T. Y., Lin, T. E., Fang, M. Y., Chen, I. J., Pathak, N., Hsu, J. T. A., Yang, J. M.* (2017) Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains , Scientific Reports , 7(1):12336. Lin, H. C., Huan, Y. S., Chu, Y. H., Liu, S. C., Shangkuan, W. C., Lai, W. S., Yang, J. M. , Lin, Y. S., Ma, K. H., Lee, J. C. (2017) Vascular anatomy is a determining factor of successful submental flap raising: a retrospective study of 70 clinical cases , PeerJ , 5:e3606. Hsu, H. H., Hsu, Y. C., Chang, L. J., Yang, J. M.* (2017) An integrated approach with new strategies for QSAR models and lead optimization , BMC Genomics , 18(Suppl 2):104. Hsu, K. C., Liu, C. Y., Lin, T. E., Hsieh, J. H., Sung, T. Y., Tseng, H. J., Yang, J. M. , Huang, W. J. (2017) Novel Class IIa-Selective Histone Deacetylase Inhibitors Discovered Using an in Silico Virtual Screening Approach , Scientific Reports , 7(1):3228. Lai, W. S., Lin, Y. Y., Shih, C. P., Chen, H. C., Yang, P. L., Chu, Y. H., Yang, J. M. , Lee, J. C. (2017) Clinical application of suction-tube-assisted septal submucosal dissection for endoscopic septoplasty , European Archives of Oto-rhino-laryngology , 274(3):1471-1475. Das, A., Adak, A. K., Ponnapalli, K., Lin, C. H., Hsu, K. C., Yang, J. M. , Hsu, T. A., Lin, C. C. (2016) Design and synthesis of 1,2,3-triazole-containing N-acyl zanamivir analogs as potent neuraminidase inhibitors , European Journal of Medicinal Chemistry , 123:397-406. Huang, K. W., Hsu, K. C., Chu, L. Y., Yang, J. M. , Yuan, H. S., Hsiao, Y. Y. (2016) Identification of Inhibitors for the DEDDh Family of Exonucleases and a Unique Inhibition Mechanism by Crystal Structure Analysis of CRN-4 Bound with 2-Morpholin-4-ylethanesulfonate (MES) , Journal of Medicinal Chemistry , 59(17):8019-29. Lin, C. H., Wu, Y. R., Yang, J. M. , Chen, W. L., Chao, C. Y., Chen, I. C., Lin, T. H., Wu, Y. C., Hsu, K. C., Chen, C. M., Lee, G. C., Hsieh-Li, H. M., Lee, C. M., Lee-Chen, G. J., (2016) Novel Lactulose and Melibiose Targeting Autophagy to Reduce PolyQ Aggregation in Cell Models of Spinocerebellar Ataxia 3 , CNS & Neurological Disorders - Drug Targets , 15(3):351-9. Tsai, W. C., Yang, J. M. , Liu, S. C., Chu, Y. H., Lai, W. S., Lin, Y. S., and Lee, J. C. (2015) Management of different kinds of head and neck defects with the submental flap for reconstruction , European Archives of Oto-Rhino-Laryngology , 272(12):3815-9. 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 , 5:10938. 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 , 48:120-30. Chao, J. I., Wang, S. P., Wu, Y. H., Yang, J. M. , Chen, CPA (2015) A novel EGFR inhibitor SP101 blocks survivin and tumor growth in the human non-small cell lung carcinoma , FASEB Journal , vol. 29 no. 1 Supplement LB113. 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 , 5:9386. 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(3):239-42. 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(1):e0116347. 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 , 15 Suppl 9:S8. (Best paper award in The 13th International Conference on Bioinformatics) 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 , 53(48):13054-8. 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 , 11:528-37. 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 , 57(14):5975-85. 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 , 53(18):2865-74. 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 , 42(2):1354-64. Liu, I. H., Lo, Y. S., and Yang, J. M.* (2013) Genome-wide structural modelling of TCR-pMHC interactions , BMC Genomics , 14 Suppl 5:S5. Chen, S. H., Lin, S. W., Lin, S. R., Liang, P. H., and Yang, J. M.* (2013) Moiety-Linkage Map Reveals Selective Nonbisphosphonate Inhibitors of Human Geranylgeranyl Diphosphate Synthase , Journal of Chemical Information and Modeling , 53(9):2299-311. 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(7):e1003127. 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 Signalling Pathway , Basic & Clinical Pharmacology & Toxicology , 113(1):8-18. 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(2):e56704. 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. Liu, I. H., Lo, Y. S. and Yang, J. M.* (2013) Template-based scoring functions for visualising biological insights of H-2K(b)-peptide-TCR complexes , International Journal of Data Mining and Bioinformatics , 8(3):326-37. 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(24):3943-8. 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 , 41(Database issue):D430-40. 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. 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(44):6327-37. 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(Web Server issue):W263-70. 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(2):139-52. 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(16):3412-9. 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(3):e33481. 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(2):e32142. 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(1):27-41. 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(3):383-8. 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(Web Server issue):W254-60. 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(7):856-65. 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. 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. 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. 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. 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(Web Server issue):W424-30. Lo, Y. S., Lin, C. Y., and Yang, J. M.* (2010) PCFamily: a web server for searching homologous protein complexes , Nucleic Acids Research , 38(Web Server issue):W516-22. 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(3):251-66. 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(3):646-62. Chen, C. C., Hwang, J. K., and Yang, J. M.* (2009) (PS)(2)-v2: template-based protein structure prediction server , BMC Bioinformatics , 10:366. 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 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(Web Server issue):W369-75. 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(2):123-31. 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. 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(9):561-6. 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(12):4268-76. 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(3):1197-210. 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(16):i14-20. 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(9):1364-73. 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. 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(5):e428. 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(Web Server issue):W438-43. 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(3):R31. 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(Web Server issue):W561-7. Yang, J. M.* , and Tung, C. H. (2006) Protein structure database search and evolutionary classification , Nucleic Acids Research , 34(13):3646-59. Chen, C. C., Hwang, J. K., and Yang, J. M.* (2006) (PS)(2): protein structure prediction server , Nucleic Acids Research , 34(Web Server issue):W152–7. 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(2):205-20. 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(4):1134-46. Yang, J. M.* , and Chen, C. C. (2004) GEMDOCK: A generic evolutionary method for molecular docking , Proteins-Structure Function and Bioinformatics , 55(2):288-304. Yang, J. M.* (2004) Development and evaluation of a generic evolutionary method for protein-ligand docking , Journal of Computational Chemistry , 25(6):843-57. 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(10):689-97. 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(4):1718-29. 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(2):69-78. 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(4):531-6. 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(3):297-311. 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(3B):655-63. 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):1-5. 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. 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(8):1897-907. Yang, J. M.* , Lin, C. J., and Kao, C. Y. (2002) A robust evolutionary algorithm for global optimization , Engineering Optimization , 34(5):405-425. Yang, J. M.* , and Kao, C. Y. (2001) Efficient evolutionary algorithm for the thin-film synthesis of inhomogeneous optical coatings , Applied Optics , 40(19):3256-67. 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(4):559-70. Yang, J. M.* , and Kao, C. Y. (2001) A robust evolutionary algorithm for training neural networks , Neural Computing & Applications , 10(3):214-30. 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(4):421-43. Yang, J. M.* , and Kao, C. Y. (2000) Integrating adaptive mutations and family competition into genetic algorithms as function optimizer , Soft Computing , 4(2):89-102. 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(3):225-37. Yang, J. M.* , and Kao, C. Y. (2000) Flexible ligand docking using a robust evolutionary algorithm , Journal of Computational Chemistry , 21(11):988-998. 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(5):333-52.

Patents

Yang, J. M. , Hsu, K. C., Sung T. Y., Lin S. R., Wang Y. M., Hsu, K. M., Lin, H. P., and Liu, W. C., Selective inhibitors for protein kinases and pharmaceutical composition and use thereof. US20160096848A1 , 2016/04/07 Chao, J. I., Wang, S. P., Chen, C. P., Yin, K. H., Yang, J. M. , and Wu, Y. H., Compound for promoting apoptosis of cancer cells and a pharmaceutical composition containing the same and uses thereof. US20160068495A1 , 2016/03/10 Wang, W. C., Cheng, W. C., and Yang, J. M. , Method of inhibiting the growth of Helicobacter pylori. US8175860B2 , 2012/05/08 楊進木、林峻宇、邱一原、李容羽、何元順、李嘉華。安非他酮和醫藥組合物在製備治療癌症之藥物的用途及抑制腫瘤細胞遷移的方法。中華民國專利：發明第 I713875號，2020/12/21。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、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。

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

李容羽 (Jung-Yu Lee)
Major Fields in BS: Animal Science
Molecular interaction networks for tumorigenesis and metastasis
E-mail: [email protected] Nikhil Pathak Pharmacy July 2020, Ph.D.
Drug Design for Pathogenic and infectious Diseases - Dengue 黃星翰
(Sing-Han Huang) Biochemical Science and Technology October 2017, Ph.D.
Human Brain Aging and Neurodegeneration Disease
Journal paper: 2 papers 林峻宇
(Chun-Yu Lin) Biological Technology July 2014, Ph.D.
Systems Biology: Protein-protein interaction
Journal paper: 11 papers 林志達
(Chih-Ta Lin) Biological Technology July 2014, Ph.D.
Anticancer drug: Kinase-specific inhibitors & networks
Journal paper: 5 papers 邱一原
(Yi-Yuan Chiu) Computer Science July 2014, Ph.D.
Computer-aided drug design
Journal paper: 4 papers 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 許凱程
(Kai-Cheng Hsu) Biological Technology July 2011, Ph.D.
Computer-aided drug design
Journal paper: 16 papers 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) 黃章維
(Jhang-Wei Huang) Biological Technology September 2010, Ph.D.
Influenza Virus: Antigenic Drift Analysis, Antigen-Antibody interaction
Journal paper: 4 papers 陳俊辰
(Chun-Chen Chen) Biological Technology June 2009, Ph.D.
Systems Biology: Protein-protein interaction
Journal paper: 3 papers 董其樺
(Chi-Hua Tung) Biological Science June 2009, Ph.D.
Structural Bioinformatics: 3D-BLAST, Antigen-Antibody interaction
Journal paper: 3 papers
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 ) 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 ) 賴文森
(Wen-Sen Lai) Department of Otolaryngology, Taichung Armed forces General Hospital June 2018, MD. Ph.D.
Journal paper: 22 papers 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

Major Fields in BS Memo (Research Groups, Research Directions, Publications) 趙千嫣
(Chien-Yen Chao) Computer Science and Information Engineering March 2019, Master
Computer-aided drug design 洪慈懋
(Tzu-Mao Hung) Nutrition March 2019, Master
Computer-aided drug design 蔡宜君
(Yi-Chun Tsai) Biological Technologyy January 2019, Master
Computer-aided drug design 巫思穎
(Szu-Ying Wu) Microbiology July 2017, Master
Computer-aided drug design 李容羽
(Jung-Yu Lee) Animal Science July 2017, Master
Systems Biology: Protein-protein interaction 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 virus Journal 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) 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

Drug discovery: Pharmalogs and Homopharma

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

Homologous structural systems biology

Structure-network GWAS

藥物傳輸老藥新用

天然藥新藥開發

抗癌與抗感染藥物開發

腦及神經老化藥物開發

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。

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。 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

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. Yang JM, Chen YF, Tu YY, Yen KR, Yang YL: Combinatorial computational approaches to identify tetracycline derivatives as flavivirus inhibitors . PLoS ONE 2007:e428. Yang JM, Chen CC: GEMDOCK: a generic evolutionary method for molecular docking . Proteins: Structure, Function, and Bioinformatics 2004, 55:288-304. Yang JM, Shen TW: A pharmacophore-based evolutionary approach for screening selective estrogen receptor modulators . Proteins: Structure, Function, and Bioinformatics 2005, 59:205-220. 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. 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. 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. Lo YS, Lin CY, Yang JM: PCFamily: a web server for searching homologous protein complexes . Nucleic Acids Research 2010, 38:W516-W522. Yang JM, Tung CH: Protein structure database search and evolutionary classification . Nucleic Acids Research 2006, 34:3646-3659. 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. Tung CH, Yang JM: fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies . Nucleic Acids Research 2007, 35:W438-W443. 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. 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. Yang JM: Development and evaluation of a generic evolutionary method for protein-ligand docking . Journal of Computational Chemistry 2004, 25:843-857. 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. 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. 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. 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.

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/

SiMMap

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

KIDFamMap

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

CaMPNets

CaMPNets: Membrane protein-regulated networks across human cancers
URL: http://campnets.life.nctu.edu.tw/

PharmaCoNets

PharmaCoNets: Drug community–regulated networks
URL: http://pharmaconets.life.nctu.edu.tw/

BioXGEM Integrated Discovery for Omics data

URL: http://140.113.120.248/BioXGEM-tools/

BioXGEM Integrated Discovery for Drug Design

URL: http://140.113.120.248/BioXGEM-drug/

FooDisNET

URL: http://140.113.120.248/FooDisNET

Tranditional Chinese Herb

Tranditional Chinese Herb
URL: http://gemdock.life.nctu.edu.tw/HERBID/

BioXGEM 常用 Data Sets

SARS-CoV-2 main protease data ( Download all )

Sequence data : Include SARS-CoV-2 main protease(fasta), 12 Coronavirus main proteases(fasta) and MSA results

Structure data : Include 57 aligned SARS-CoV main proteases(pdb) and 187 aligned SARS-CoV-2 main proteases(pdb)

FDA approved drugs : Include 2125 approved drugs from DrugBank(mol)

Selected docking poses : Include 8 docking poses of different PPCs

Molecular recognition

100 PDB complexes set : 100 protein-ligand complexes

CCDC/Astex test set : 305 protein-ligand complexes

Virtual screening sets

Thymidine kinase inhibitors : 10 known inhibitors for thymidine kinase

Estrogen receptor alpha agonists : 10 known agonists for estrogen receptor alpha

Estrogen receptor alpha antagonists : 10 known antagonists of estrogen receptor alpha

Dihydrofolate reductase inhibitors : 10 known ligands for human dihydrofolate reductase

Human carbonic anhydrase II (HCAII) : 20 inhibitors of human carbonic anhydrase II

ACD 990 dataset : 990 randomly selected compounds from ACD

CMC database : 7375 pharmaceutical compounds (1900 - present) from Comprehensive Medicinal Chemistry (CMC)

Gene expression sets

Breast cancer

Breast cancer_100 genes : 150 samples (30N,120P) with 100 genes for teaching

Breast cancer_all genes : 150 samples (30N,120P) with 20531 genes for comprehensive analysis

Breast cancer_clinical : TCGA clinical information of breast cancer patients

Liver cancer

Liver cancer_100 genes : 150 samples (50N,100P) with 100 genes for teaching

Liver cancer_all genes : 150 samples (50N,100P) with 20531 genes for comprehensive analysis

Liver cancer_clinical : TCGA clinical information of liver cancer patients

Head and neck cancer

Head and neck cancer_100 genes : 120 samples (40N,80P) with 100 genes for teaching

Head and neck cancer_all genes : 120 samples (40N,80P) with 20531 genes for comprehensive analysis

Head and neck cancer_clinical : TCGA clinical information of head and neck cancer patients

Diabetes

Diabetes_100 genes : 17 samples (9N,8P) with 100 genes for teaching

Diabetes_all genes : 17 samples (9N,8P) samples with 14463 genes for comprehensive analysis

Convolutional neural network for human cancer types prediction

Source code of CNN model and example samples : The zip file contained three programs and example samples for building CNN model

Useful Links for Paper (Thesis) Writing and Research Career Advice

How to be a Good Graduate Student/Advisor , by Marie desJardins

You and Your Research [ English.pdf ] [ Chinese.pdf ] by Richard W. Hamming

Useful Things To Know about Ph.D. Thesis Research by H. T. Kung

Better Dissertation Writing in English from Prof. Yuh-Dauh Lyuu's homepage

How to Organize your Thesis , by John W. Chinneck

Writing and Presenting Your Thesis or Dissertation , by S. Joseph Levine, Ph.D.

The Elements of Style, 4th ed. by William Strunk, Jr., E.B. White, and Roger Angell. The 1918 version (free) .

The Chicago Manual of Style

Research career advice from David Patternson's homepage

Protein

This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. UniProt The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. PDBsum The PDBsum is a pictorial database that provides an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank (PDB). It shows the molecule(s) that make up the structure (ie protein chains, DNA, ligands and metal ions) and schematic diagrams of their interactions. Extensive use is made of the freely available RasMol molecular graphics program to view the molecules and their interactions in 3D. CATH is a classification of protein structures downloaded from the Protein Data Bank. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Proteins are generally composed of one or more functional regions, commonly termed domains. Different combinations of domains give rise to the diverse range of proteins found in nature. The identification of domains that occur within proteins can therefore provide insights into their function. Dali Database The Dali Database is based on all-against-all 3D structure comparison of protein structures in the Protein Data Bank (PDB). The structural neighbourhoods and alignments are automatically maintained and regularly updated using the Dali search engine. SWISS-MODEL SWISS-MODEL is a fully automated protein structure homology-modelling server. (PS) ² (PS) ² is an automatic homology modeling server. The ConSurf Server It provides evolutionary conservation profiles for proteins of known structure in the PDB. The Human Protein Atlas portal is a publicly available database with millions of high-resolution images showing the spatial distribution of proteins in 44 different normal human tissues and 20 different cancer types, as well as 46 different human cell lines. STRING STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources: Genomic Context, High-throughput Experiments, (Conserved) Coexpression and Previous Knowledge. Brenda The comprehensive enzyme information system PhosphoSitePlus PhosphoSitePlus® (PSP) is an online systems biology resource providing comprehensive information and tools for the study of protein post-translational modifications (PTMs) including phosphorylation, ubiquitination, acetylation and methylation. BLAST For blast search to find similar DNA or Protein sequences CLUSTAL Omega and other MSA tools For Protein MSA T-Coffee T-Coffee is a multiple sequence alignment program. Its main characteristic is that it will allow you to combine results obtained with several alignment methods. WebLogo WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible. WebLogo 3 WebLogo is a web based application designed to make the generation of sequence logos easy and painless. Back to top PubChem PubChem is a database of chemical molecules and their activities against biological assays. ChEMBL It is a manually curated chemical database of bioactive molecules with drug-like properties. DrugBank The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug. BindingDB BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. STITCH STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Avogadro Molecule building and editing tool to build and minimize compound structures TCMID Provide information on all respects of Traditional Chinese Medicine including formulae, herbs and herbal ingredients Dr. Duke's Phytochemical and Ethnobotanical Databases Provide the infomation about plants and their ingredients. Provide the infomation about plants in Bangladesh and their ingredients. A free database of commercially-available compounds. MolPort MolPort is advanced chemical marketplace. Selleckchem Selleck Chemicals supplies over 3,000 inhibitors used in the study of cell signaling pathways. We actively tracks the latest science so our customers can rely on us to be the leading supplier of the newest inhibitors. Chemical Book 查詢化合物相關資訊的網站 Back to top Gene Ontology The Gene Ontology (GO) project is a major bioinformatics initiative to develop a computational representation of our evolving knowledge of how genes encode biological functions at the molecular, cellular and tissue system levels. Gene Expression Data (L1000) Gene expression is highly correlated. We take advantage of this high degree of correlation to reduce the number of measurements needed to generate meaningful gene expression data for the approximately 20,000 genes in the human genome. DAVID DAVID now provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes. GEO (Gene Expression Omnibus) GEO is a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles. Genome This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations. 1000 Genome Browser A global reference for human genetic variation TCGA (The Cancer Genome Atlas) The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. cBioPortal The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets (e.g. TCGA). CCLE (Cancer Cell Line Encyclopedia) The Cancer Cell Line Encyclopedia (CCLE) project is an effort to conduct a detailed genetic characterization of a large panel of human cancer cell lines. The CCLE provides public access analysis and visualization of DNA copy number, mRNA expression, mutation data and more, for 1000 cancer cell lines. GeneCards GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. It automatically integrates gene-centric data from ~125 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information. Provide integrated information of domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. Allen Brain Atlas An anatomically comprehensive atlas of the adult human brain transcriptome Provide integrated genetic, genomic, and biological data for mouse. Provide integrated biological information for the budding yeast Saccharomyces cerevisiae. ArrayExpress ArrayExpress Archive of Functional Genomics Data stores data from high-throughput functional genomics experiments, and provides these data for reuse to the research community. Back to top Cytoscape Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. MeV is a versatile microarray data analysis tool, incorporating sophisticated algorithms for clustering, visualization, classification, statistical analysis and biological theme discovery. GENE-E GENE-E is a matrix visualization and analysis platform designed to support visual data exploration. Back to top KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks. EBI (The European Bioinformatics Institute) EMBL-EBI provides freely available data from life science experiments, performs basic research in computational biology and offers an extensive user training programme, supporting researchers in academia and industry. COSMIC All cancers arise as a result of the acquisition of a series of fixed DNA sequence abnormalities, mutations, many of which ultimately confer a growth advantage upon the cells in which they have occurred. There is a vast amount of information available in the published scientific literature about these changes. COSMIC is designed to store and display somatic mutation information and related details and contains information relating to human cancers. Ensembl Including Gene expression database, SNP database and ENCODE (Encyclopedia of DNA Elements (ENCODE) Consortium)
*The Encyclopedia of DNA Elements (ENCODE) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI) RefSeq: NCBI Reference Sequence Database A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein. ExPASy ExPASy is the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. On this portal you find resources from many different SIB groups as well as external institutions. SMART SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. More than 500 domain families found in signalling, extracellular and chromatin-associated proteins are detectable. These domains are extensively annotated with respect to phyletic distributions, functional class, tertiary structures and functionally important residues. Each domain found in a non-redundant protein database as well as search parameters and taxonomic information are stored in a relational database system. User interfaces to this database allow searches for proteins containing specific combinations of domains in defined taxa. For all the details, please refer to the publications on SMART. BioPharma Insight BioPharm Insight is your definitive guide to the global life sciences community, combining an online business intelligence system of comprehensive market analytics and key industry contacts with an independent investigative journalism news service. GlobalData GlobalData is the premier source of actionable insight into the energy and healthcare industries. With the combined expertise of more than 1,000 researchers, market analysts and consultants, we provide high-quality, accurate and transparent industry insight that helps our clients to achieve growth and increase business value. Genetic Engineering & Biotechnology News (GEN) has retained its position as the premier biotech publication since its launch in 1981. GEN publishes a print edition 21 times a year and has additional exclusive editorial content online, including news and analysis as well as webinars, videos, and polls. GEN's unique news and technology focus covers the entire bioproduct life cycle, including drug discovery, early-stage R&D, applied research (e.g., omics, biomarkers, and diagnostics), bioprocessing, and commercialization. Phys Org: Biology news 海峽生技醫藥品風雲