StreptomeDB: a resource for natural compounds isolated from Streptomyces species

Xavier Lucas, Christian Senger, Anika Erxleben, Björn A. Grüning, Kersten Döring, Johannes Mosch, Stephan Flemming, Stefan Günther (Lead / Corresponding author)

Research output: Contribution to journalArticlepeer-review

66 Citations (Scopus)
182 Downloads (Pure)

Abstract

Bacteria from the genus Streptomyces are very important for the production of natural bioactive compounds such as antibiotic, antitumour or immunosuppressant drugs. Around two-thirds of all known natural antibiotics are produced by these bacteria. An enormous quantity of crucial data related to this genus has been generated and published, but so far no freely available and comprehensive database exists. Here, we present StreptomeDB (http://www.pharmaceutical-bioinformatics.de/streptomedb/). To the best of our knowledge, this is the largest database of natural products isolated from Streptomyces. It contains >2400 unique and diverse compounds from >1900 different Streptomyces strains and substrains. In addition to names and molecular structures of the compounds, information about source organisms, references, biological role, activities and synthesis routes (e.g. polyketide synthase derived and non-ribosomal peptides derived) is included. Data can be accessed through queries on compound names, chemical structures or organisms. Extraction from the literature was performed through automatic text mining of thousands of articles from PubMed, followed by manual curation. All annotated compound structures can be downloaded from the website and applied for in silico screenings for identifying new active molecules with undiscovered properties.

Original languageEnglish
Pages (from-to)D1130-D1136
Number of pages7
JournalNucleic Acids Research
Volume41
Issue numberDatabase issue
Early online date28 Nov 2012
DOIs
Publication statusPublished - 1 Jan 2013

Keywords

  • Databases, Chemical
  • Drug discovery
  • Drug resistance, Bacterial
  • Internet
  • Streptomyces
  • Journal article
  • Research support, Non-U.S. Gov't

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