Standard reaction Gibbs energy estimation for biochemical reactions
Requirements (for the python version):
- python == 2.7
- numpy >= 1.6.2
- scipy >= 0.14
- oct2py >= 3.1 (dependent on Octave)
- Open-Babel >= 2.3.1 ('babel' must be in PATH, including python bindings)
- ChemAxon's Marvin >= 5.11 ('cxcalc' must be in PATH)
Requirements (for the MATLAB version):
- Matlab >= 7
- python == 2.7
- numpy >= 1.6.2
- scipy >= 0.14
- Open-Babel >= 2.3.1 ('babel' must be in PATH, including python bindings)
- ChemAxon's Marvin >= 5.11 ('cxcalc' must be in PATH)
For more information on the method behind component-contribution, please view our open access paper:
Noor E, Haraldsdóttir HS, Milo R, Fleming RMT (2013) Consistent Estimation of Gibbs Energy Using Component Contributions, PLoS Comput Biol 9:e1003098, DOI: 10.1371/journal.pcbi.1003098
Please, quote this paper if you publish work that uses component-contribution.
- compounds.tsv - table of all KEGG compounds, their name and InChI (used only in Matlab code)
- fixed_mapping.tsv - table mapping some KEGG compound IDs to BiGG IDs (overriding the InChI-based mapping)
- formation_energies_transformed.tsv - table of biochemical formation energies (used for training CC)
- kegg_additions.tsv - table of compounds that are missing from KEGG together with their InChI
- kegg_compounds.json.gz - JSON of all KEGG compounds including their InChI and names
- redox.tsv - table of reduction potentials (used for training CC)
- TECRDB.tsv - table of K'eq values from the NIST database (http://xpdb.nist.gov/enzyme_thermodynamics/)