Table 1.
Tools for natural product pathway discovery, prediction and analysis.
| Name | Description | Web Address |
|---|---|---|
| Cluster mining tools | ||
| antiSMASH | Web application to mine and analyze bacterial and fungal genome for secondary metabolite BGCs | https://antismash.secondarymetabolites.org (accessed on 5 July 2021) |
| Mibig 2.0 | A robust community standard for annotation of metadata on BGCs and their molecular products | https://mibig.secondarymetabolites.org/ (accessed on 5 July 2021) |
| ClusterCAD | A database and web-based toolkit to harness the potential of type I modular polyketide synthases for combinatorial biosynthesis | https://clustercad.jbei.org/ (accessed on 5 July 2021) |
| PRISM 3 | Web for prediction of genetically encoded NRPs and PKs | http://magarveylab.ca/prism/ (accessed on 5 July 2021) |
| RODEO | Algorithm developed to identify ribosomally synthesized and post-translationally modified peptide BGCs | http://www.ripprodeo.org (accessed on 7 July 2021) |
| Bagel2 | Annotation of putative bacteriocins and antibiotics from genomic DNA | http://bagel2.molgenrug.nl/ (accessed on 7 July 2021) |
| CLUSEAN | Identification of domains and prediction of specificities for PKS and NRPS genes | https://bitbucket.org/tilmweber/clusean (accessed on 7 July 2021) |
| SBSPKS | Structural modeling of PKS modules and identification of key residues in the interfaces between modular PKS subunits | http://www.nii.ac.in/sbspks.html (accessed on 10 July 2021) |
| SMURF | Annotation of PKS, NRPS, NRPS-PKS hybrid, indole alkoloid and terpene BGCs from fungal genomic DNA | http://jcvi.org/smurf/index.Php (accessed on 10 July 2021) |
| 2metDB | A tool offers the possibility to identify PKS and NRPS BGCs | http://secmetdb.sourceforge.net/ (accessed on 10 July 2021) |
| ClusterFinder | A tool to detect putative BGCs in genomic and metagenomic data | https://github.com/petercim/ClusterFinder (accessed on 10 July 2021) |
| eSNaPD | A tool to survey BGCs diversity in metagenomic DNA sequences | http://esnapd2.rockefeller.edu/ (accessed on 10 July 2021) |
| EvoMining | Web for phylogenomics to identify BGCs | http://148.247.230.39/newevomining/new/evomining_web/index.html (accessed on 13 July 2021) |
| MIDDAS-M | A tool that uses genome and transcriptome data to identify BGCs in fungal genomes | http://133.242.13.217/MIDDAS-M/ (accessed on 13 July 2021) |
| MIPS-CG | Web application to identify BGCs with genome data | http://www.fung-metb.net/ (accessed on 13 July 2021) |
| IMG-ABC | Database of experimentally verified and predicted BGCs across 40,000 isolated microbial genomes | https://img.jgi.doe.gov/abc/ (accessed on 13 July 2021) |
| NaPDoS | Web for offering analysis of PKS/NRPS | http://napdos.ucsd.edu/ (accessed on 15 July 2021) |
| PKS/NRPS analytic tools | ||
| NP.searcher | Web application to identify PKS and NRPS BGCs | http://dna.sherman.lsi.umich.edu (accessed on 15 July 2021) |
| ClustScan | Web accessible database for PKS/NRPS BGCs | http://csdb.bioserv.pbf.hr/csdb/ClustScanWeb.html (accessed on 19 July 2021) |
| GNP | Web application to identify BGCs (mainly PKS/NRPS) | http://magarveylab.ca/gnp/ (accessed on 19 July 2021) |
| NRPS-PKS | Web application to identify PKS BGCs | http://www.nii.res.in/nrps-pks.html (accessed on 19 July 2021) |
| Specificity predictors for NRPS or PKS | ||
| NRPS/PKS substrate predictor | Web for predicting A-domain or AT-domain | http://www.cmbi.ru.nl/NRPS-PKS-substrate-predictor/ (accessed on 21 July 2021) |
| LSI-based A-domain function predictor | Web for predicting A-domain | http://bioserv7.bioinfo.pbf.hr/LSIpredictor/AdomainPrediction.jsp (accessed on 21 July 2021) |
| NRPSsp | Web for predicting A-domain | http://www.nrpssp.com/ (accessed on 21 July 2021) |
| ASMPKS | Web for identification of PKS genes from genomic DNA | http://gate.smallsoft.co.kr:8008/pks/ (accessed on 21 July 2021) |
| PKS/NRPS Web Server/Predictive Blast Server | Web for predicting A-domain specificities | http://nrps.igs.umaryland.edu/nrps/ (accessed on 21 July 2021) |
| Compounds databases | ||
| ChEBI | A database and ontology of chemical compounds focusing on small molecules | https://www.ebi.ac.uk/chebi/ (accessed on 21 July 2021) |
| ChEMBL | A database providing information on bioactive molecules with drug-like properties | https://www.ebi.ac.uk/chembl/ (accessed on 21 July 2021) |
| ChemSpider | A database providing information on structures and properties of over 35 million structures | http://www.chemspider.com/ (accessed on 21 July 2021) |
| KNApSAcK database | A database on compound information of more than 50,000 natural products of plants and microorganisms | http://kanaya.aist-nara.ac.jp/KNApSAcK/ (accessed on 21 July 2021) |
| PubChem | A database contains synthetic compounds as well as natural products | http://pubchem.ncbi.nlm.nih.gov/ (accessed on 21 July 2021) |
| Metabolomics tools | ||
| GNPS | Web for analyzing mass spectrometry (MS)/MS data | http://gnps.ucsd.edu/ (accessed on 21 July 2021) |
| GNP/iSNAP | Web application to automatically identify metabolites in MS/MS data | http://magarveylab.ca/gnp/ (accessed on 21 July 2021) |
| NRPquest | Web for correlating NRP data with gene clusters | http://cyclo.ucsd.edu (accessed on 21 July 2021) |
| Pep2Path | Web for correlating peptide sequence tags with NRP and post-translationally modified peptide BGCs | http://pep2path.sourceforge.net (accessed on 21 July 2021) |