ArticleNucleic acids research2017
SeMPI: a genome-based secondary metabolite prediction and identification web server.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 30 citations in OpenAlex.
- The Cytotoxic Properties of Extreme Fungi's Bioactive Components-An Updated Metabolic and Omics Overview.Life (Basel, Switzerland) · 2023Review
- How to Completely Squeeze a Fungus-Advanced Genome Mining Tools for Novel Bioactive Substances.Pharmaceutics · 2022Review
- Genetic Relationships in the Toxin-Producing Fungal Endophyte,Journal of fungi (Basel, Switzerland) · 2021Article
- StreptomeDB 3.0: an updated compendium of streptomycetes natural products.Nucleic acids research · 2021Article
- SeMPI 2.0-A Web Server for PKS and NRPS Predictions Combined with Metabolite Screening in Natural Product Databases.Metabolites · 2020Article
- DDAP: docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases.Bioinformatics (Oxford, England) · 2020Article
- Fungal secondary metabolism: regulation, function and drug discovery.Nature reviews. Microbiology · 2019Review
- Concepts and Methods to Access Novel Antibiotics from Actinomycetes.Antibiotics (Basel, Switzerland) · 2018Review
- ClusterCAD: a computational platform for type I modular polyketide synthase design.Nucleic acids research · 2018Article
- Microbiome and metabolome data integration provides insight into health and disease.Translational research : the journal of laboratory and clinical medicine · 2017Review
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The secondary metabolism of bacteria, fungi and plants yields a vast number of bioactive substances. The constantly increasing amount of published genomic data provides the opportunity for an efficient identification of gene clusters by genome mining. Conversely, for many natural products with resolved structures, the encoding gene clusters have not been identified yet. Even though genome mining tools have become significantly more efficient in the identification of biosynthetic gene clusters, structural elucidation of the actual secondary metabolite is still challenging, especially due to as yet unpredictable post-modifications. Here, we introduce SeMPI, a web server providing a prediction and identification pipeline for natural products synthesized by polyketide synthases of type I modular. In order to limit the possible structures of PKS products and to include putative tailoring reactions, a structural comparison with annotated natural products was introduced. Furthermore, a benchmark was designed based on 40 gene clusters with annotated PKS products. The web server of the pipeline (SeMPI) is freely available at: http://www.pharmaceutical-bioinformatics.de/sempi.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.