component-contribution
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eladnoor
Standard reaction Gibbs energy estimation for biochemical reactions
Hi Elad, I tried to use the recache_compound.py to add new components that are not in the KEGG database. An error message is displayed in the chemaxon.py file (see attached...
Now, we issue "fake" IDs that look like KEGG, with high numbers (e.g. C80067). This is confusing and should be changed to something like COCO:C00001 (COCO for COmponent-COntribution).
The new main key for matching compounds is the InChIKey. This works very well across databases, but only when the compound has a structure. Unfortunately, we also have thermodynamic information...
Apparently, in the NIST database the compound 5-dehydroshikimate should be mapped to KEGG compound C02637, instead of C02652. The reason is that 5-dehydroshikimate belongs to an older nomenclature and is...
Allow the KEGG input file to contain "free" electrons (C05359) by creating a syntax for specifying their reduction potential. This can potentially replace having a long list of electron carriers...
Reactions that have 0 group change but shouldn't: 1) FMN(ox) = FMN(red) 2) FAD(ox) = FAD(red) 3) ATP + ADP = AMP + A-Tetra-P (in this case, it seems that...