Graph-based |
ReTrace |
KEGG |
Bipartite graph |
Atom mapping |
Heuristic search |
Atom conservation and pathway length |
[23] |
PathComp |
KEGG |
Substrate graph |
– |
Depth-first search (DFS) |
– |
[26] |
MetaRoute |
KEGG |
Reaction graph |
Weighted graph and atom mapping |
Eppstein's k-shortest path |
Atom conservation and metabolite connectivity |
[51] |
Pathway Hunter Tool |
KEGG |
Substrate graph |
– |
Breadth-first search (BFS) with (Higher-order horn logic) HOHL |
Structure similarity and pathway length |
[63] |
FMM |
KEGG |
Substrate graph |
Manual cofactor removal |
BFS |
Compare pathway across organisms |
[64] |
RouteSearch |
MetaCyc |
Substrate graph |
Atom mapping |
Branch and Bound |
Atom conservation and pathway length |
[65] |
MRE |
KEGG |
Substrate graph |
Weighted graph |
Yen's loopless k-shortest path |
Thermodynamics and genes from host organism |
[66] |
CMPF |
KEGG, RPAIR |
Bipartite graph |
Weighted graph |
Bounded depth path enumeration |
Metabolite connectivity, reaction occurrence frequency, and pathway switching |
[67] |
NeAT |
MetaCyc |
Bipartite graph |
Weighted graph |
Takahashi–Matsuyama, Pairwise K-shortest paths, and kWalks |
Metabolite connectivity |
[68] |
LPAT/BPAT |
KEGG |
Bipartite graph |
Atom mapping |
BPAT-M Search |
Atom conservation and pathway length |
[69], [139]
|
Rahnuma |
KEGG |
Hypergraph |
Phylogeny or sub-network |
DFS |
– |
[70] |
Metabolic Tinker |
CHEBI, Rhea |
Hypergraph |
Weighted graph |
Heuristic search |
Pathway length, structure similarity, and thermodynamics |
[71] |
FogLight |
KEGG, MetaCyc |
Hypergraph |
And/Or graph |
Brute-force search |
Pathway length |
[73] |
MRSD |
KEGG |
substrate graph |
Weighted graph |
Eppstein's k-shortest path |
Reaction occurrence frequency |
[78] |
DESHARKY |
KEGG |
– |
Phylogeny |
Monte Carlo |
Metabolic burden |
[88] |
Stoichiometry-based |
optStoic |
KEGG, MetRxn |
S matrix |
Design overall stoichiometry |
MILP |
Pathway length or total metabolic flux |
[24] |
PathTracer |
BIGG, iJO1366 |
Substrate graph, S matrix |
Atom mapping (MapMaker) |
MILP |
Pathway length or most active path |
[50] |
CFP |
BIGG |
Substrate graph, S matrix |
Atom mapping (carbon exchange network) |
MILP |
Pathway length |
[75] |
METATOOL 5.0/k-shortest EFM |
BIGG, iAF1260 |
S matrix |
– |
MILP |
Pathway length |
[76], [89]
|
OptStrain |
KEGG |
S matrix |
– |
MILP |
Number of heterologous reactions |
[99] |
Retrosynthesis-based |
Simpheny |
BIGG |
Substrate graph |
molecule sizes |
Retrosynthetic enumeration |
Pathway length, thermodynamics, product yield, number of known metabolites/enzymes, and existence of reaction operators |
[5] |
GEM-Path |
BIGG, iJO1366 |
Substrate graph |
Third level EC number and substrate similarity |
Retrosynthetic enumeration |
Thermodynamics and product yield |
[57] |
XTMS/RetroPath/RetroPath 2.0 |
MetaCyc, BioCyc |
S matrix |
Molecular signature with predetermined distance |
Retrosynthetic enumeration and MILP |
Thermodynamics, gene prediction, pathway length, number of putative steps, and product yield |
[52], [82], [84]
|
BNICE |
KEGG, ATLAS |
Substrate graph |
Qualitative/Quantitative pruning |
Retrosynthetic enumeration |
Pruning criteria assessment (thermodynamics, pathway length, etc.) |
[8], [53]
|
UM-PPS |
UM-BBD |
Substrate graph |
Rule priority |
Retrosynthetic enumeration |
– |
[56] |
PathPred |
KEGG, RPAIR |
Substrate graph |
Structure similarity |
Retrosynthetic enumeration |
Compound similarity and pathway score |
[54] |
Route Designer |
MOS, Beilste Crossfile |
Substrate graph |
Heuristics and user defined limits |
Retrosynthetic enumeration |
Weighted function (wastage, example counts, and balanced disconnections.) |
[55] |
SimIndex/SimZyme |
BRENDA |
Substrate graph |
Structure similarity |
Byers–Waterman type pathway search |
Pathway length |
[83] |
Method by Cho et al. |
KEGG |
Substrate graph |
– |
Retrosynthetic enumeration |
Combination of five priority factors |
[22] |