Pathway search
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Introduce source and target compound inchikey (can be retrieved from PubChem):
Source compound INCHIKEY (first 14 letters, comma-separated, max 15 compounds)
Target compound INCHIKEY (first 14 letters)
Network parameters
Modify distances within the network:
Prefer pathways through known reactions
Prefer more atom conservative pathways
Truncate the network to exclude connections with low atom conservation:
Atom conservation threshold: {{ carThreshold }}
Pathway search parameters
Importance of:
Enzyme availability (BridgIT score)
Atom conservation
Keeping pathways as short as possible
Avoiding novel reactions
Maximum number of pathways in the output: {{ numIntSeqs * numRxnAlt * numEnzAlt }}
Number of alternative sequences of the intermediates: {{ numIntSeqs }}
Number of reactions per reactant-product pair: {{ numRxnAlt }}
Number of EC class alternatives per reaction: {{ numEnzAlt }}
Compound filtering
Charge
Charge min
Charge max
Bonds
Number of rotatable bonds min
Number of rotatable bonds max
Triple bonds
Atom types
C min
C max
O min
O max
N min
N max
P min
P max
S min
S max
Halogens
F min
F max
Cl min
Cl max
I min
I max
Br min
Br max
Metalloids and other non-metals
B min
B max
Si min
Si max
As min
As max
Se min
Se max
Ring types
benzene min
benzene max
pyridine min
pyridine max
pyrimidine min
pyrimidine max
pyridazine min
pyridazine max
imidazole min
imidazole max
imidazole cation min
imidazole cation max
pyrrole min
pyrrole max
pyrazine min
pyrazine max
furan min
furan max
pyrazole min
pyrazole max
isoxazole min
isoxazole max
isoxazole cation min
isoxazole cation max
thiophene min
thiophene max
oxazole min
oxazole max
thiazole min
thiazole max
thiazole cation min
thiazole cation max
1,2,3,4-tetrazole min
1,2,3,4-tetrazole max
1,2,3,5-tetrazole min
1,2,3,5-tetrazole max
1,3,4-triazole min
1,3,4-triazole max
1,2,3-triazole min
1,2,3-triazole max
1,2,4-triazole min
1,2,4-triazole max
1,3,4-thiadiazole min
1,3,4-thiadiazole max
1,2,3-thiadiazole cation min
1,2,3-thiadiazole cation max
other ring types min
other ring types max
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