Network of chemical reactions between biochemical compounds

The files here have been generated using this software. Please cite the following paper in any work that has resulted from using these data sets:

Lower glycolysis carries a higher flux than any biochemically possible alternative, S. J. Court, B. Waclaw, R. J. Allen, Nature Communications 6 (2015),8427, doi:10.1038/ncomms9427.

Files (CHOPN molecules)

The files have been created using the full set of reactions described in our paper, and C,H,O,P, and N atoms.

List of chemical compounds

Files "compounds*.dat" contain lists of chemical compounds with different maximal number of carbon atoms. Their structure is very simple:
column 1 = compound index
column 2 = Free energy of formation [kJ/mol, standard conditions: concentration = 1M, pH=0, T=298K]
column 3 = chemical formula of the compound
column 4 = common name (if any) or "---"
column 5 = charge in the water solution if all protons dissociate

Reaction network

The format for the reaction network "reactions*.dat" is
column 1 = reaction type
column 2 = substrate index
column 3 = product index
column 4 = no. of ATP molecules produced (negative if consumed)
column 5 = no. of NADH molecules produced (negative if consumed)
column 6 = free energy change [kJ/mol] in this reaction at standard conditions
columns 7,... = chemical reaction in a human-readable form

Data files: up to 3 carbon atoms, up to 4 carbon atoms

Files (CHOP molecules)

These files contain a slightly smaller set of reactions and do not include nitrogen-containing compounds (only C,H,O, and P), but they have additional clevage reactions in which a larger molecule is split into two smaller molecules. The format of the reaction network file is
column 1 = free energy change [kJ/mol] at standard conditions
columns 2,...n+1 = indices of n substrates of a given reaction
column n+2 = ">" denotes the direction of the reaction
columns n+3,...,n+2+m = m indices for the products of the reaction

Data files: up to 3 carbon atoms, up to 4 carbon atoms, up to 6 carbon atoms