TIPdb-3D: The three-dimensional structure database of phytochemicals from Taiwan indigenous plants

Database

Volumn 2014, Issue , 2014, Pages

  Tung, Chun Wei ^a,b   Lin, Ying Chi ^a   Chang, Hsun Shuo ^a   Wang, Chia Chi ^a,b   Chen, Ih Sheng ^a   Jheng, Jhao Liang ^a,b   Li, Jih Heng ^a,b  

^a KAOHSIUNG MEDICAL UNIVERSITY   (Taiwan)

^b NATIONAL HEALTH RESEARCH INSTITUTES   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84987657364     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bau055     Document Type: Article

References (27)

1. Mishra, B.B. and Tiwari, V.K. (2011) Natural products: an evolving role in future drug discovery. Eur. J. Med. Chem., 46, 4769-4807.
2. Newman, D.J. and Cragg, G.M. (2012) Natural products as sources of new drugs over the 30 years from 1981 to 2010. J. Nat. Prod., 75, 311-335.
3. Saklani, A. and Kutty, S.K. (2008) Plant-derived compounds in clinical trials. Drug Discov. Today, 13, 161-171.
4. Huang, T.C. Flora of Taiwan. Editorial Committee of the Flora of Taiwan: Taipei, Taiwan, 1993-2003.
5. Li, H.J., Jiang, Y. and Li, P. (2006) Chemistry, bioactivity and geographical diversity of steroidal alkaloids from the Liliaceae family. Nat. Prod. Rep., 23, 735-752.
6. Lin, Y.C., Wang, C.C., Chen, I.S. et al. (2013) TIPdb: a database of anticancer, antiplatelet, and antituberculosis phytochemicals from indigenous plants in Taiwan. Scientific World Journal, 2013, 736386.
7. Tung, C.W. (2014) Public databases of plant natural products for computational drug discovery. Curr. Comput.-Aided Drug Des., doi: 10.2174/1573409910666140414145934.
8. Saxena, S., Devi, P.B., Soni, V. et al. (2014) Identification of novel inhibitors against Mycobacterium tuberculosis L-alanine dehydrogenase (MTB-AlaDH) through structure-based virtual screening. J. Mol. Graph. Model., 47, 37-43.
9. Chen, C.Y. (2011) TCM Database@Taiwan: the world's largest traditional Chinese medicine database for drug screening in silico. PLoS One, 6, e15939.
10. Nakamura, K., Shimura, N., Otabe, Y. et al. (2013) KNApSAcK-3D: a three-dimensional structure database of plant metabolites. Plant Cell Physiol., 54, e4.
11. Maeda, M.H. and Kondo, K. (2013) Three-dimensional structure database of natural metabolites (3DMET): a novel database of curated 3D structures. J. Chem. Inf. Model, 53, 527-533.
12. Valli, M., dos Santos, R.N., Figueira, L.D. et al. (2013) Development of a natural products database from the biodiversity of Brazil. J. Nat. Prod., 76, 439-444.
13. Afendi, F.M., Okada, T., Yamazaki, M., et al. (2012) KNApSAcK family databases: integrated metabolite-plant species databases for multifaceted plant research. Plant Cell Physiol., 53, e1.
14. Kanehisa, M., Goto, S., Sato, Y. et al. (2014) Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res., 42, D199-D205.
15. Lipinski, C.A., Lombardo, F., Dominy, B.W. et al. (2001) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug. Deliv. Rev., 46, 3-26.
16. Puranen, J.S., Vainio, M.J. and Johnson, M.S. (2010) Accurate conformation-dependent molecular electrostatic potentials for high-throughput in silico drug discovery. J. Comput. Chem., 31, 1722-1732.
17. Vainio, M.J. and Johnson, M.S. (2007) Generating conformer ensembles using a multiobjective genetic algorithm. J. Chem. Inf. Model., 47, 2462-2474.
18. Lagorce, D., Pencheva, T., Villoutreix, B.O. et al. (2009) DG-AMMOS: a new tool to generate 3d conformation of small molecules using distance geometry and automated molecular mechanics optimization for in silico screening. BMC Chem. Biol., 9, 6.
19. O'Boyle, N.M., Banck, M., James, C.A. et al. (2011) Open Babel: an open chemical toolbox. J. Cheminform., 3, 33.
20. AMMP program. http://www.cs.gsu.edu/~cscrwh/ammp/ammp.html (9 March 2014, date last accessed).
21. Halgren, T.A. (1996) Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. J. Comput. Chem., 17, 490-519.
22. Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/ (9 March 2014, date last accessed).
23. Yap, C.W. (2011) PaDEL-descriptor: an open source software to calculate molecular descriptors and fingerprints. J. Comput. Chem., 32, 1466-74.
24. Steinbeck, C, Han, Y., Kuhn, S. et al. (2003) The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics. J. Chem. Inf. Comput. Sci., 43, 493-500.
25. Kuhn, M., Szklarczyk, D., Pletscher-Frankild, S. et al. (2014) STITCH 4: integration of protein-chemical interactions with user data. Nucleic Acids Res., 42, D401-D407.
26. Davis, A.P., Wiegers, T.C., Roberts, P.M. et al. (2013) A CTD-Pfizer collaboration: manual curation of 88, 000 scientific articles text mined for drug-disease and drug-phenotype interactions. Database (Oxford), 2013, bat080.
27. Mathias, S.L., Hines-Kay J., Yang J.J. et al. (2013) The CARLSBAD database: a confederated database of chemical bio-activities. Database (Oxford), 2013, bat044.