Databases focused on natural products and 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
CAMPR3 also provides information on antimicrobial peptides.
ChEBI (Chemical Entities of Biological Interest) is a general database and ontology of chemical compounds largely focused on small molecules.
- de Matos, P., et al., 2012, Methods Mol. Biol., 803:273-96
- Hill, D.P., et al., 2013, BMC Genomics 14:513
- Hastings, J., et al., 2013, Nucleic Acids Res. 41(Database issue):D456-63
- Hastings, J., et al., 2016, Nucleic Acids Res. 44:D1214-9
ChEMBL is a database providing information on bioactive molecules with drug-like properties.
- Gaulton, A., et al., 2012, Nucleic Acids Res. 40(Database issue):D1100-7
- McGlinchey, S., et al., 2014, Nucleic Acids Res. 42(Database issue):D1083-90
- Papadatos, G. and Overington, J.P., 2014, Future Med. Chem. 6:361-4
- Davies, M., et al., 2015, Nucleic Acids Res. 43(W1):W612-20
- Gaulton, A., et al., 2017, Nucleic Acids Res. 45:D945-D954
database, compounds, structures
ChemSpider is a chemical database providing information on structures and properties of over 35 million structures from hundreds of data sources.
- Little, J.L., et al., 2012, J. Am. Soc. Mass Spectrom. 23:179-85
- "Editorial: ChemSpider--a tool for Natural Products research", 2015, Nat. Prod. Rep. 32:1163-4
database, compounds, structures
DBAASPv.2 also provides information on antimicrobial peptides.
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.
- Bolton, E., et al. (2008). Annual Reports in Computational Chemistry, Volume 4. Washington, DC, American Chemical Society. 4:217-241
- Condurso, H. L. and Bruner, S. D., 2012, Nat. Prod. Rep. 29:1099-110
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., 2016, Nucleic Acids Res. 44:D509-14