Abstract
This paper describes the characteristics and functionalities of the web-based database NAPROC-13 ( http://c13.usal.es ). It contains Carbon NMR spectral data from more than 21.000 Natural Products and related derivates. A considerable number of structures included in the database have been revised and corrected from the original publications considering subsequent published revisions. It provides tools that facilitate the structural identification of natural compounds even before their purification. This database allows for flexible searches by chemical structure, substructure of structures as well as spectral features, chemical shifts and multiplicities. Searches for names, formulas, molecular weights, family, type and group of compound according to the IUPAC classification are also implemented. It supports a wide range of searches, from simple text matching to complex boolean queries. These capabilities are used together with visual interactive tools, which enable the structural elucidation of known and unknown compounds by comparison of their 13C NMR data.
Financial support came from the Ministerio de Educación y Ciencia, project TIN2006-06313 and the Junta de Castilla y León, project SA221U13. Research also supported by Spanish project Strongsoft TIN2012-39391-C04-04.
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References
Bohlmann, F., Zdero, C., Jakupovic, J., Grenz, M., et al.: Further Pyrrolizidine alkaloids and furoeremophilanes from Senecio species. Phytochemistry 25, 1151–1159 (1986)
Breitmaier, E., Woelter, W.: Carbon-13 NMR spectroscopy. High-resolution methods and applications in Organic Chemistry. VCH Publ., Weinheim (1987)
Chen, J., Swamidass, S.J., Dou, Y., et al.: Chemdb: a public database of small molecules and related chemoinformatics resources. Bioinformatics 21, 4122–4139 (2005)
Clarkson, C., Stærk, D., Hansen, S.H., Smith, P.J., Jaroszewski, J.W.: Discovering new natural products directly from crude extracts by HPLC-SPE-NMR: chinane diterpenes in Harpagophytum procumbens. J. Nat. Prod. 69, 527–530 (2006)
Cui, Q., Lewis, I.A., Hegeman, A.D., Anderson, M.E., et al.: Metabolite identification via the Madison Metabolomics Consortium Database. Nat. Biotechnol. 26, 162–164 (2008)
Ertl, P., Jacob, O.: WWW-based chemical information system. J. Mol. Struct. Theochem. 419, 113–120 (1997)
Gasteiger, J.: Chemoinformatics: a new field with a long tradition. Anal. Bioanal. Chem. 384, 57–64 (2006)
Grabley, S., Thiericke, R.: Bioactive agents from natural sources: trends in discovery and application. Adv. Biochem. Eng. Biotechnol. 64, 101–154 (1999)
Halabalaki, M., Vougogiannopoulou, K., Mikros, E., Skaltsounis, A.L.: Recent advances and new strategies in the NMR-based identification of natural products. Curr. Opin. Biotechnol. 25, 1–7 (2014)
Harvey, A.: Strategies for discovering drugs from previously unexplored natural products. Drug. Discov. Today 5, 294–300 (2000)
Inselberg, A.: The plane with parallel coordinates. The Visual Computer 1, 69–91 (1985)
Kochev, N., Monev, V., Bangov, I.: Searching chemical structures. In: Chemoinformatics: a Textbook, pp. 291–318. Wiley-VCH (2003)
Lei, J., Zhou, J.: J. Chem. Inf. Comput. Sci. 42, 742–748 (2002)
López-Pérez, J.L., Theron, R., del Olmo, E., Díez, D., Vaquero, M., Adserias, J.F.: Application of chemoinformatics to the structural elucidation of natural compounds. In: Corchado, E., Yin, H., Botti, V., Fyfe, C. (eds.) IDEAL 2006. LNCS, vol. 4224, pp. 1150–1157. Springer, Heidelberg (2006)
López-Pérez, J.L., Theron, R., Olmo, E., del Díaz, D.: NAPROC-13: a database for the dereplication of natural product mixtures in bioassay-guided protocols. Bioinformatics 23, 3256–3257 (2007)
Peláez, R., Theron, R., García, C.A., López-Pérez, J.L., et al.: Design of new chemoinformatic tools for the analysis of virtual screening studies: Application to tubulin inhibitors. In: Corchado, J.M., De Paz, J.F., Rocha, M.P., Riverola, F.F. (eds.) IWPACBB 2008. ASC, vol. 49, pp. 189–196. Springer, Heidelberg (2008)
Robien, W.: NMR data correlation with chemical structure. In: von Ragu Schleyer, P., Allinger, N.L., Clark, T., Gasteiger, J., Kollman, P.A., Schaefer, H.F. (eds.) Encyclopedia of Computational Chemistry, vol. 3, pp. 1845–1857. Wiley, New York (1998)
Scalbert, A., Andres-Lacueva, C., Arita, M., Kroon, P., et al.: Databases on food phytochemicals and their health-promoting effects. J. Agric. Food Chem. 59, 4331 (2011)
Shoichet, B.K.: Virtual screening of chemical libraries. Nature 432, 862–865 (2004)
Steinbeck, C., Kuhn, S.: NMRShiftDB compound identification and structure elucidation support through a free community-built web database. Phytochemistry 65, 2711–2717 (2004)
Theron, R., Olmo, E., del, D.D., Vaquero, M., Adserias, J.F., López-Pérez, J.L.: NATPRO-C13: an interactive tool for the structural elucidation of natural compounds. In: Corchado, E., Corchado, J.M., Abraham, A. (eds.) Innovations Hybrid Intelligent Systems. ASC, vol. 44, pp. 401–410. Springer, Heidelberg (2008)
Ulrich, E.L., Akutsu, H., Doreleijers, J.F., Harano, Y., Ioannidis, Y.E., Lin, J., et al.: BioMagResBank. Nucleic Acids Res. 36, D402–D408 (2008)
Urones, J.G., Barcala, P.B., Marcos, I.S., Moro, R.F., Esteban, M.L., et al.: Pyrrolizidine alkaloids from Senecio gallicus and S. adonidifolius. Phytochemistry 27, 1507–1510 (1988)
Weininger, D.: Smiles, a chemical language and information system. 1. Introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci. 28, 31–36 (1988)
Wishart, D.S., Jewison, T., Guo, A.C., Wilson, M., Knox, C., et al.: HMDB 3.0—The Human Metabolome Database in 2013. Nucleic Acids Res. 41(D1), D801–D807 (2013)
Witte, L., Ernst, L., Wray, V., Hartmann, T.: Revised structure of the main alkaloid of Senecio adonidifolius. Phytochemistry 31, 1027–1028 (1992)
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López-Pérez, J.L. et al. (2014). NAPROC-13: A Carbon NMR Web Database for the Structural Elucidation of Natural Products and Food Phytochemicals. In: Saez-Rodriguez, J., Rocha, M., Fdez-Riverola, F., De Paz Santana, J. (eds) 8th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2014). Advances in Intelligent Systems and Computing, vol 294. Springer, Cham. https://doi.org/10.1007/978-3-319-07581-5_2
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DOI: https://doi.org/10.1007/978-3-319-07581-5_2
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