Genomics & Informatics

  • 제7권4호
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  • Pages.212-216
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  • 2009
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  • 1598-866X(pISSN)
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  • 2234-0742(eISSN)
한국유전체학회 (Korea Genome Organization)
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WebChemDB: An Integrated Chemical Database Retrieval System

  • 발행 : 2009.12.31
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초록

WebChemDB is an integrated chemical database retrieval system that provides access to over 8 million publicly available chemical structures, including related information on their biological activities and direct links to other public chemical resources, such as PubChem, ChEBI, and DrugBank. The data are publicly available over the web, using two-dimensional (2D) and three-dimensional (3D) structure retrieval systems with various filters and molecular descriptors. The web services API also provides researchers with functionalities to programmatically manipulate, search, and analyze the data.

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참고문헌

  1. Ahn, C. (2007). Pharmacogenomics in Drug Discovery and Development. Genomics & Informatics 5, 41-45
  2. Butina, D. (1999). Unsupervised Data Base Clustering Based on Daylight's Fingerprint and Tanimoto Similarity: A Fast and Automated Way To Cluster Small and Large Data Sets. J. Chem. Inf. Comput. Sci. 39, 747-750 https://doi.org/10.1021/ci9803381
  3. Carr, R.A., Congreve, M., Murray, C.W., and Rees, D.C. (2005). Fragment-based lead discovery: leads by design. Drug Discov. Today 10, 987-992 https://doi.org/10.1016/S1359-6446(05)03511-7
  4. Chen, J., Swamidass, S.J., Dou, Y., Bruand, J., and Baldi, P. (2005). ChemDB: a public database of small molecules and related chemoinformatics resources. Bioinformatics 21, 4133-4139 https://doi.org/10.1093/bioinformatics/bti683
  5. Csizmadia, F. (2000). JChem: Java applets and modules supporting chemical database handling from web browsers. J. Chem. Inf. Comput. Sci. 40, 323-324 https://doi.org/10.1021/ci9902696
  6. Degtyarenko, K., de Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcántara, R., Darsow, M., Guedj, M., and Ashburner, M. (2008). ChEBI: a database and ontology for chemical entities of biological interest. Nucl. Acids Res. 36, 344-350 https://doi.org/10.1093/nar/gkm791
  7. Hull, D., Wolstencroft, K., Stevens, R., Goble, C., Pocock, M.R., Li, P., and Oinn, T. (2006). Taverna: a tool for building and running workflows of services. Nucl. Acids Res. 1, 729-732 https://doi.org/10.1093/nar/gkl320
  8. Irwin, J.J., and Shoichet, B.K. (2005). ZINC-a free database of commercially available compounds for virtual screening. J. Chem. Inf. Comput. Sci. 45, 177-182 https://doi.org/10.1021/ci049714+
  9. Kanehisa, M., and Goto, S. (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucl. Acids Res. 28, 27-30 https://doi.org/10.1093/nar/28.1.27
  10. Kang, T.S., Woo, S.W., Park, H.J., Han, S.Y., Park, M.H., and Chung, M.W. (2009). The Korean Pharmacogenomic Database at NIFDS: 2008 Update. Genomics & Informatics 7, 163-167 https://doi.org/10.5808/GI.2009.7.3.163
  11. Lipinski, J. (2000). Drug-like properties and the causes of poor solubility and poor permeability. J. Pharmacol. Toxicol. Methods 44, 235-249 https://doi.org/10.1016/S1056-8719(00)00107-6
  12. Michael, R.B., Nicolas, C., Fabian, D., Thomas, R.G., Tobias, K., Thorsten, M., Peter, O., Christoph, S., Kilian, T., and Bernd, W. (2008). KNIME: The Konstanz Information Miner. Data Analysis, Machine Learning and Applications 319-326 https://doi.org/10.1007/978-3-540-78246-9_38
  13. Raymond, J. W., and Willett, P. (2003). Similarity searching in databases of flexible 3D structures using smoothed bounded distance matrices. J. Chem. Inf. Comput. Sci. 43, 908-916 https://doi.org/10.1021/ci034002p
  14. Richard, A.M., and Williams, C.R. (2002). Distributed structure-searchable toxicity (DSSTox) public database network: a proposal. Mutat. Res. 499, 27-52 https://doi.org/10.1016/S0027-5107(01)00289-5
  15. Shuichi, K., Toshiaki, K., Yoko, S., and Minoru, K. (2003). KEGG API: A Web Service Using SOAP/WSDL to Access the KEGG System. Genome Informatics 14, 673-674
  16. Steinbeck, C., and Kuhn, S. (2004). NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database. Phytochemistry 65, 2711-2717 https://doi.org/10.1016/j.phytochem.2004.08.027
  17. Steinbeck, C., Han, Y. Q., Kuhn, S., Horlacher, O., Luttmann, E., and Willighagen, E.L. (2003). The Chemistry Development Kit (CDK): An open-source Java library for chemo- and bioinformatics. J. Chem. Inf. Comput. Sci. 43, 493-500 https://doi.org/10.1021/ci025584y
  18. Teague, S.J., Davis, A.M., Leeson, P.D., and Oprea, T. (1999). The Design of Leadlike Combinatorial Libraries. Angew. Chem. Int. Ed. Engl. 38, 3743-3748 https://doi.org/10.1002/(SICI)1521-3773(19991216)38:24<3743::AID-ANIE3743>3.0.CO;2-U
  19. Voigt, J.H., Bienfait, B., Wang, S., and Nicklaus, M.C. (2001). Comparison of the NCI open database with seven large chemical structural databases. J. Chem. Inf. Comput. Sci. 41, 702-712 https://doi.org/10.1021/ci000150t
  20. Wang, Y., Xiao, J., Suzek, T.O., Zhang, J., Wang, J., and Bryant, S.H. (2009). PubChem: a public information system for analyzing bioactivities of small molecules. Nucl. Acids Res. 37, 623-633 https://doi.org/10.1093/nar/gkp456
  21. Weininger, D., Weininger, A., and Weininger, L.J. (1989). SMILES. 2. Algorithm for generation of uniques SMILES notation. J. Chem. Inf. Comput. Sci. 29, 97-101 https://doi.org/10.1021/ci00062a008
  22. Wishart, D.S. (2008). DrugBank and its relevance to pharmacogenomics. Pharmacogenomics. 9, 1155-1162 https://doi.org/10.2217/14622416.9.8.1155