Drug Discovery and Development via Synthetic Biology - Synthetic Biology - page 175

TABLE 10.1 Tools for Natural Product Pathway Discovery, Prediction, and Analysis
Tool Full Name Description Web Address

antiSMASH Anti biotics & S econdary

M etabolite A nalysis
Sh ell

Annotation of biosynthetic gene clusters
for many secondary metabolites from
genomic DNA, including polyketides,
nonribosomal peptides, terpenes,
aminoglycosides, aminocoumarins,
indolocarbazoles, lantibiotics,
bacteriocins, nucleosides, beta-lactams,
butyrolactones, siderophores, melanins,
and others. Includes comparative gene
cluster analysis

http://antismash.
secondarymetabolites.
org/

ASMPKS A nalysis S ystem for

M odular P oly k etide
S ynthesis

Identification of PKS genes from genomic
DNA, prediction of domain architecture,
and visualization of predicted polyketide
products. Also includes a database
of known polyketides

http://gate.smallsoft.co.
kr:8008/pks/

Bagel2 Ba cteriocin Ge nome

Mining Too l 2

Annotation of putative bacteriocins and
lantibiotics from genomic DNA. Includes
a database of validated bacteriocins

http://bagel2.molgenrug.nl/

CLUSEAN Clu ster Se quence

An alyzer

Identification of domains and prediction of
specificities for PKS and NRPS genes

http://redmine.
secondarymetabolites.
org/projects/clusean

ClustScan Clust er Scan ner Annotation and product structure

prediction for PKS, NRPS, and hybrid
NRPS/PKS genes from genomic DNA.
Includes stereochemistry prediction

http://bioserv.pbf.hr/cms/
index.php?
page

clustscan/

5

NORINE No n r ibosomal peptides

(with ' ine ' as a typical
ending of peptide
names)

Database of more than 1100 peptides
containing structural information as well
as biological activity, producing
organisms, and literature references

http://bioinfo.lifl.fr/norine/

186

NP.Searcher N atural P roduct Searcher Automated annotation and product

structure prediction for PKS, NRPS,
and hybrid NRPS/PKS genes from
genomic DNA

http://dna.sherman.lsi.
umich.edu/

NRPS-PKS PKS, NRPS, and hybrid NRPS/PKS

domain identification and specificity
prediction, as well as a database of
characterized gene clusters

http://www.nii.res.in/
nrps-pks.html

NRPSpredictor2 Prediction of adenylation domain specificity

based on 10-amino-acid Stachelhaus
code and 8-angstrom signature. Includes
bacterial and fungal prediction

http://nrps.informatik.
uni-tuebingen.de/

PKS-NRPS
Analysis
Website

Identification of PKS and NRPS domains,
as well as adenylation domain specificity
prediction based on the 8-amino-
acid code

http://nrps.igs.umaryland.
edu/nrps/

SBSPKS S tructure B ased

S equence Analysis of
P oly k etide S ynthases

Structural modeling of PKS modules
and identification of key residues in
the interfaces between modular
PKS subunits. Also includes all
functionalities and database support
of the NRPS-PKS tool

http://www.nii.ac.in/
sbspks.html

SMURF S econdary M etabolite

U nique R egions F inder

Annotation of polyketide, non-ribosomal
peptide, NRPS-PKS hybrid, indole
alkoloid, and terpene biosynthetic gene
clusters from fungal genomic DNA,
including prediction of borders

http://jcvi.org/smurf/index.
php