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Secondary metabolite biosynthetic pathway software tools & databases | drug discovery

Natural products of bacteria and fungi are the most important source for antimicrobial drug leads. For decades, such compounds were exclusively found by chemical/bioactivity-guided screening approaches. The rapid progress in sequencing technologies…
ClusterFinder
Desktop

ClusterFinder

Predicts biosynthetic gene clusters in genomes. The software detects gene…

Predicts biosynthetic gene clusters in genomes. The software detects gene clusters irrespective of whether they belong to known or a priori specified classes. It exhibits relatively little training…

RODEO
Web
Desktop

RODEO Rapid ORF Description and Evaluation Online

Helps biosynthetic gene cluster (BGC) analysis, with an emphasis on ribosomal…

Helps biosynthetic gene cluster (BGC) analysis, with an emphasis on ribosomal natural product (RiPP) discovery. RODEO combines hidden-Markov-model-(HMM) based analysis, heuristic scoring, and machine…

antiSMASH-DB
Dataset

antiSMASH-DB

Provides a collection of state-of the art annotated biosynthetic gene cluster…

Provides a collection of state-of the art annotated biosynthetic gene cluster (BGC) data. antiSMASH-DB enables to perform cross-genome analyses by offering complex queries on the data sets. It offers…

IMG-ABC
Dataset

IMG-ABC Integrated Microbial Genomes-Atlas of Biosynthetic gene Clusters

Offers experimentally verified and predicted biosynthetic gene clusters (BCs).…

Offers experimentally verified and predicted biosynthetic gene clusters (BCs). IMG-ABC database contains more than 730000 BCs in 40034 isolate microbial genomes and more than 310000 BCs in 2416…

MIBiG
Format

MIBiG Minimum Information about a Biosynthetic Gene cluster

Facilitates consistent and systematic deposition and retrieval of data on…

Facilitates consistent and systematic deposition and retrieval of data on biosynthetic gene clusters. MIBiG standard covers general parameters that are applicable to each and every gene cluster as…

antiSMASH
Desktop
Web

antiSMASH antibiotics & Secondary Metabolite Analysis Shell

Aligns the identified regions at the gene cluster level to their nearest…

Aligns the identified regions at the gene cluster level to their nearest relatives from a database containing all other known gene clusters. antiSMASH facilitates the mining of bacterial and fungal…

PhytoClust
Web

PhytoClust

Detects candidate metabolic gene clusters in plant genomes. The PhytoClust…

Detects candidate metabolic gene clusters in plant genomes. The PhytoClust algorithm employs several enzyme families related to plant specialized metabolism, translated into hidden Markov models…

NaPDoS
Web

NaPDoS

Detects and analyzes secondary metabolite genes. NaPDoS is especially designed…

Detects and analyzes secondary metabolite genes. NaPDoS is especially designed to concern (detection and extraction) C- and KS- domains from DNA or amino acid sequence data. This includes metagenomic…

EvoMining
Web

EvoMining

Performs phylogenomic analyses to identify expansions on central metabolic…

Performs phylogenomic analyses to identify expansions on central metabolic enzyme families and their recruitment by NP biosynthetic pathways in an unbiased manner. EvoMining is an evolutionary-driven…

PRISM
Web

PRISM PRediction Informatics for Secondary Metabolomes

A computational resource for the identification of biosynthetic gene clusters,…

A computational resource for the identification of biosynthetic gene clusters, prediction of genetically encoded nonribosomal peptides and type I and II polyketides, and bio- and cheminformatic…

SMIPS
Web
Desktop

SMIPS

Predicts secondary metabolite (SM) anchor genes, also called SM backbone genes,…

Predicts secondary metabolite (SM) anchor genes, also called SM backbone genes, in protein sequences. SMIPS is a webserver for genome-wide detection of SM key enzymes ('anchor' genes):…

A2MDB
Dataset

A2MDB Aspergillus Secondary Metabolite Database

Gathers on Aspergillus genus and especially on its secondary metabolites and…

Gathers on Aspergillus genus and especially on its secondary metabolites and their biological interactions. A2MDB provides information about data related to Aspergillus ITS sequences, metabolites and…

RiPPMiner
Dataset

RiPPMiner

Represents a bioinformatics resource concerning deciphering chemical structures…

Represents a bioinformatics resource concerning deciphering chemical structures of ribosomally synthesized and post-translationally modified peptides (RiPPs) through genome mining. The RiPPMiner…

SeMPI
Web

SeMPI

Follows an ab-initio approach and predicts the correct order of the substrates…

Follows an ab-initio approach and predicts the correct order of the substrates which constitute the secondary metabolite. SeMPI is a web server that successfully combines and complements available…

clusterTools
Desktop

clusterTools

Aids in the characterization of putative biosynthetic gene clusters (BGCs).…

Aids in the characterization of putative biosynthetic gene clusters (BGCs). clusterTools organizes genomic information on coding sequences in a way that enables directed, hypothesis-driven queries…

SBSPKS
Web

SBSPKS

A webserver for carrying out sequence and structure based analysis of…

A webserver for carrying out sequence and structure based analysis of Polyketide Synthases, an important family of multifunctional megasynthases involved in the biosynthesis of a variety of…

NRPSpredictor
Web
Desktop

NRPSpredictor Non-Ribosomal Peptide Synthetases predictor

Predicts A-domain specificity using Support Vector Machines (SVM) on four…

Predicts A-domain specificity using Support Vector Machines (SVM) on four hierarchical levels, ranging from gross physicochemical properties of an A-domain’s substrates down to single amino acid…

SEARCHPKS
Web

SEARCHPKS

Facilitates easy identification of various polyketide synthase (PKS) domains…

Facilitates easy identification of various polyketide synthase (PKS) domains and modules from a given polypeptide sequence. SEARCHPKS is a software for detection and analysis of PKS domains in a…

ClusterMine360
Dataset

ClusterMine360

A database of microbial polyketide and non-ribosomal peptide gene clusters.…

A database of microbial polyketide and non-ribosomal peptide gene clusters. ClusterMine360 takes advantage of crowd-sourcing by allowing members of the community to make contributions while…

DoBISCUIT
Dataset

DoBISCUIT Database of BIoSynthesis clusters CUrated and InTegrated

A literature-based, manually curated database of gene clusters for secondary…

A literature-based, manually curated database of gene clusters for secondary metabolite biosynthesis. DoBISCUIT integrates the latest literature information and provides standardized…

ClustScan-Profe…
Desktop

ClustScan-Professional

An integrated suite of computer programs that take a "top down"…

An integrated suite of computer programs that take a "top down" approach to the annotation of gene clusters encoding thiotemplate modular systems (TMS). ClustScan-Professional can analyse…

CASSIS
Web
Desktop

CASSIS cluster assignment by islands of sites

Exploits the idea of co-regulation of the cluster genes, which assumes the…

Exploits the idea of co-regulation of the cluster genes, which assumes the existence of common regulatory patterns in the cluster promoters. CASSIS requires two input files: (i) genome sequence…

NRPSsp
Desktop
Web

NRPSsp Non-Ribosomal Peptide Synthase substrate predictor

Applies a new approach in the areas of, the prediction based on HMM, enlarged…

Applies a new approach in the areas of, the prediction based on HMM, enlarged training sets applying mining techniques, the regular update of its database and its design for the functional analysis…

MIDDAS-M
Web

MIDDAS-M

A motif-independent de novo detection algorithm for secondary metabolite…

A motif-independent de novo detection algorithm for secondary metabolite biosynthetic (SMB) gene clusters. MIDDAS-M enables the comprehensive exploration of functional SMB genes in fungal genomes by…

SMURF
Web

SMURF Secondary Metabolite Unique Regions Finder

A web-based tool that finds secondary metabolite biosynthesis genes and…

A web-based tool that finds secondary metabolite biosynthesis genes and pathways in fungal genomes. The predictions are based on PFAM and TIGRFAM domain content as well as on a gene's…

CLUSEAN
Desktop

CLUSEAN CLUster SEquence ANalyzer

Helps to annotate and analyze such gene clusters. CLUSEAN integrates standard…

Helps to annotate and analyze such gene clusters. CLUSEAN integrates standard analysis tools, like BLAST and HMMer, with specific tools for the identification of the functional domains and motifs in…

PKMiner
Dataset

PKMiner

A comprehensive computational analysis of type II PKSs and their gene clusters…

A comprehensive computational analysis of type II PKSs and their gene clusters in actinobacterial genomes. PKMiner is useful for research in the discovery of novel bacterial aromatic polyketides.

NP.searcher
Desktop
Web

NP.searcher Natural products search engine

Scans rapidly microbial genomes for secondary metabolite biosynthetic gene…

Scans rapidly microbial genomes for secondary metabolite biosynthetic gene clusters, and output candidate nonribosomal peptide and polyketide natural products in SMILES format, enabling immediate…

PKSIIIexplorer
Web

PKSIIIexplorer

A web server based on 'transductive support vector machine' that…

A web server based on 'transductive support vector machine' that allows fast and reliable prediction of Type III polyketide synthase proteins. Users can submit their protein sequences in…

r-CSDB
Dataset

r-CSDB recombinant ClustScan database

Contains information about predicted recombinants between polyketide synthases…

Contains information about predicted recombinants between polyketide synthases (PKS clusters). The recombinants are generated by modeling homologous recombination and are associated with annotation…

CSDB
Dataset

CSDB ClustScan database

Contains highly annotated descriptions of 170 clusters. CSDB has a hierarchical…

Contains highly annotated descriptions of 170 clusters. CSDB has a hierarchical organization, which allows easy extraction of DNA and protein sequences of polypeptides, modules, and domains as well…

ASMPKS
Web

ASMPKS

Supports computational analysis of the modular polyketide synthase(PKS) for…

Supports computational analysis of the modular polyketide synthase(PKS) for genome sequences. ASMPKS is a system that provides overall management of information on modular PKS, including PKS database…

FunGeneClusterS
Web
Desktop

FunGeneClusterS

Predict clusters with more than 10 genes and allows identification of…

Predict clusters with more than 10 genes and allows identification of co-regulated gene clusters irrespective of the function of the genes. FunGeneClusterS is a web application implemented as a…

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