Databases focussed on natural products / compounds¶
Please note: In addition to the resources listed here, there exist several commercial databases. If there is no possibility to freely access their data, these databases are not included in this list.
Search chemical structure (in SMILE format) against antibioticome to determin potential target of the molecule.
Antimicrobial Peptide Database¶
The Antimicrobial Peptide Database (APD) contains ~2700 antimicrobial peptides and (small proteins <200 aa) from prokaryotic and eukaryotic organisms. The searchable hand-curated database contains information on the peptide sequences, post-translational modifications, nomenclature, properties, targets, links to peptide sequence records / 3D structures (PDB), when available. In addition to the database, the APD web-page also provides a tools section with links to software and web-pages useful for antimicrobial peptide research.
- Wang, Z. and Wang, G., 2004, Nucleic Acids Res. 32:D590-2
- Wang, G., et al., 2009, Nucleic Acids Res. 37:D933-7
- Wang, G., et al., 2016, Nucleic Acids Res. 44:D1087-93
ChEBI (Chemical Entities of Biological Interest) is a general database and ontology of chemical compounds largely focused on small molecules.
- Hastings, J., et al., 2015, Nucleic Acids Res. pii:gkv1031
- Hill, D.P., et al., 2013, BMC Genomics 14:513
- Hastings, J., et al., 2013, Nucleic Acids Res. 41(Database issue):D456-63
- de Matos, P., et al., 2012, Methods Mol. Biol., 803:273-96
ChEMBL is a database providing information on bioactive molecules with drug-like properties.
- Davies, M., et al., 2015, Nucleic Acids Res. 43(W1):W612-20
- Papadatos, G. and Overington, J.P., Future Med. Chem. 6:361-4
- McGlinchey, S., et al., 2014, Nucleic Acids Res. 42(Database issue):D1083-90
- Gaulton, A., et al., 2012, Nucleic Acids Res. 40(Database issue):D1100-7
database, compounds, structures
ChemSpider is a chemical database providing information on structures and properties of over 35 million structures from hundreds of data sources.
- "Editorial: ChemSpider--a tool for Natural Products research", 2015, Nat. Prod. Rep. 32:1163-4
- Little, J.L., et al., 2012, J. Am. Soc. Mass Spectrom. 23:179-85
database, compounds, structures
The KNApSAcK family of databases contains compound information of more than 50,000 natural products of plants, but also of microorganisms.
- Afendi, F. M., et al., 2012, Plant Cell Physiol. 53:e1
- Nakamura, Y., et al., 2014, Plant Cell Physiol. 55:e7
PubChem is a repository of more than 20 million small-molecule compounds, their properties and biological activities. The database contains synthetic compounds as well as natural products.
- Condurso, H. L. and Bruner, S. D., 2012, Nat. Prod. Rep. 29:1099-110
- Bolton, E., et al. (2008). Annual Reports in Computational Chemistry, Volume 4. Washington, DC, American Chemical Society. 4:217-241
NORINE is a curated database on non-ribosomally synthesized peptides, activities and literature references. Currently, NORINE has more than 1,100 entries.
- Caboche, S., et al., 2008, Nucleic Acids Res. 36:D326-D331
- Caboche, S., et al., 2009, BMC Struct.Biol 9:15
- Caboche, S., et al., 2010, J. Bacteriol. 192:5143-50
- Abdo, A., et al., 2012, J. Comput. Aided Mol. Des. 26:1187-94
- Pupin, M., et al., 2015, Synth. Syst. Biotechnol. 1:89-94
- Flissi, A., et al., 2016, Nucleic Acids Res. 44:D1113-8
- Leclère, V., et al., 2016, Methods Mol Biol. 1401:209-32
database, compounds, non-ribsomal peptides, activities
Novel Antibiotics Database¶
The Novel Antibiotics database contains information about compounds that were published in the Journal of Antbiotics until 2008.
- http://www.antibiotics.or.jp/journal/database/database-top.htm Novel Antibiotics Data Base data files download
- http://www0.nih.go.jp/~jun/NADB/search.html (online search tool; link currently not working)
StreptomeDB is a comprehensive database on metabolites of Streptomycetes. Currently, the database contains entries for more than 4000 natural products, 2500 producers, 900 activities. (For details, see StreptomeDB statistics page
- Lucas, X., et al., 2013, Nucleic Acids Res. 41:D1130-6
- Klementz, D., et al., 2015, Nucleic Acids Res. 44:D509-14