Table 2 Pathway prediction systems

UM-PPS

Predicts microbial degradation pathways for xenobiotic compounds based on biotransformation rules.

[17]

PathPred

Predicts pathways for microbial biodegradation of environmental compounds and biosynthesis of plant secondary metabolites.

[18]

Biochemical Network Integrated Computational Explorer (BNICE)

Predicts novel thermodynamic feasible pathways on the basis of reaction rules of the enzyme commission classification system.

[19, 63]

DESHARKY

A Monte Carlo algorithm that identifies metabolic pathways from target compounds using a database of known enzymatic reactions. Also provides amino acid sequences of corresponding enzymes from phylogenetically closely related organisms.

[64]

From Metabolite to Metabolite (FMM)

Online tool that predicts the pathway between two compounds based on the KEGG database.

[21]

CarbonSearch

Algorithm that identifies pathways within existing metabolic networks by tracking the conservation of atoms moving through them.

[65]

OptStrain

Computational framework that advises on optimization of the host’s metabolic network to add a particular metabolic pathway by adding or deleting reactions

[66]

Metabolic Tinker

Predicts all paths between two compounds

[21]