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Review
. 2016 Feb 5;1(2):69-79.
doi: 10.1016/j.synbio.2015.12.002. eCollection 2016 Jun.

The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production

Tilmann Weber  1 , Hyun Uk Kim  1   2
Affiliations
Review

The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production

Tilmann Weber et al. Synth Syst Biotechnol. .

Abstract

Natural products are among the most important sources of lead molecules for drug discovery. With the development of affordable whole-genome sequencing technologies and other 'omics tools, the field of natural products research is currently undergoing a shift in paradigms. While, for decades, mainly analytical and chemical methods gave access to this group of compounds, nowadays genomics-based methods offer complementary approaches to find, identify and characterize such molecules. This paradigm shift also resulted in a high demand for computational tools to assist researchers in their daily work. In this context, this review gives a summary of tools and databases that currently are available to mine, identify and characterize natural product biosynthesis pathways and their producers based on 'omics data. A web portal called Secondary Metabolite Bioinformatics Portal (SMBP at http://www.secondarymetabolites.org) is introduced to provide a one-stop catalog and links to these bioinformatics resources. In addition, an outlook is presented how the existing tools and those to be developed will influence synthetic biology approaches in the natural products field.

Keywords: A, adenylation domain; Antibiotics; BGC, biosynthetic gene cluster; Bioinformatics; Biosynthesis; C, condensation domain; GPR, gene-protein-reaction; HMM, hidden Markov model; LC, liquid chromatography; MS, mass spectrometry; NMR, nuclear magnetic resonance; NRP, non-ribosomally synthesized peptide; NRPS; NRPS, non-ribosomal peptide synthetase; Natural product; PCP, peptidyl carrier protein; PK, polyketide; PKS; PKS, polyketide synthase; RiPP, ribosomally and post-translationally modified peptide; SVM, support vector machine.

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Figures

Fig. 1
Fig. 1
Overview of the most commonly used and freely accessible tools specialized for the analysis of secondary metabolites and their pathways.
Fig. 2
Fig. 2
A screenshot of the antiSMASH page in the Secondary Metabolite Bioinformatics Portal at http://www.secondarymetabolites.org.
See this image and copyright information in PMC

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