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Nucleic Acids Res. 2016 Jan 4;44(D1):D509-14. doi: 10.1093/nar/gkv1319. Epub 2015 Nov 28.

StreptomeDB 2.0--an extended resource of natural products produced by streptomycetes.

Author information

1
Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Strasse 9, Freiburg 79104, Germany.
2
Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Strasse 9, Freiburg 79104, Germany School of Life Sciences, Division of Biological Chemistry and Drug Discovery, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, UK.
3
Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Strasse 9, Freiburg 79104, Germany Chair for Bioinformatics, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, Freiburg 79110, Germany.
4
Pharmaceutical Biology, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, 79104 Freiburg, Germany.
5
Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Strasse 9, Freiburg 79104, Germany stefan.guenther@pharmazie.uni-freiburg.de.

Abstract

Over the last decades, the genus Streptomyces has stirred huge interest in the scientific community as a source of bioactive compounds. The majority of all known antibiotics is isolated from these bacterial strains, as well as a variety of other drugs such as antitumor agents, immunosuppressants and antifungals. To the best of our knowledge, StreptomeDB was the first database focusing on compounds produced by streptomycetes. The new version presented herein represents a major step forward: its content has been increased to over 4000 compounds and more than 2500 host organisms. In addition, we have extended the background information and included hundreds of new manually curated references to literature. The latest update features a unique scaffold-based navigation system, which enables the exploration of the chemical diversity of StreptomeDB on a structural basis. We have included a phylogenetic tree, based on 16S rRNA sequences, which comprises more than two-thirds of the included host organisms. It enables visualizing the frequency, appearance, and persistence of compounds and scaffolds in an evolutionary context. Additionally, we have included predicted MS- and NMR-spectra of thousands of compounds for assignment of experimental data. The database is freely accessible via http://www.pharmaceutical-bioinformatics.org/streptomedb.

PMID:
26615197
PMCID:
PMC4702922
DOI:
10.1093/nar/gkv1319
[Indexed for MEDLINE]
Free PMC Article

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