At present, in IMAC, metabolites and reactions are numbered according to the definitions in the LIGAND database1,2, and atoms in metabolites are numbered according to unique SMILES notation3. To get the numbers for atoms in most metabolites, mol files in the LIGAND database were converted into SMILES strings using Marvin4 with the options for aromatization and removal of explicit Hydrogen atoms.
The basic concept of the IMAC database is described in several documents, which include the references 5, 6, 7 and 8 shown below. Please cite them accordingly when making use of the IMAC database.
The above database, IMAC, has been developed by Jun Ohta. The copyright of IMAC belongs solely to Jun Ohta. IMAC is distributed in the hope that it will be useful,
but without any warranty. Jun Ohta does not assume any legal responsibility for accuracy or usefulness of any information in IMAC.
1 Goto, S., Nishioka, T., and Kanehisa, M., "LIGAND: Chemical Database for Enzyme Reactions", Bioinformatics, 14:591-599 (1998).
2 Goto, S., Okuno, Y., Hattori, M., Nishioka, T., and Kanehisa, M., "LIGAND: database of chemical compounds and reactions in biological pathways", Nucleic Acids Research, 30:402-404 (2002).
3 Weininger, D., Weininger, A., and Weininger, J. L., "SMILES 2. Algorithm for Generation of Unique SMILES Notation", J. Chem. Inf. Comput. Sci., 29:97-101 (1989).
4 Marvin is a product of ChemAxon Ltd., Máramaros köz 3/a, Budapest, 1037 Hungary (www.chemaxon.com).
5 Ohta, J., "Data Format for Computational Analysis of Intermetabolite Atom-level Connectivity in Metabolic Networks", Molecular & Cellular Proteomics 2(9), 830-830 (2003)
6 Ohta, J., "Atom-level Analysis of Metabolic Networks using GNU Octave and IMAC, A Database of Inter-Metabolite Atom-level Connectivity", Proceedings for 2nd International E.Coli Alliance Conference on Systems Biology, XLI (2004)
7 Ohta, J., "Toward Complete Structural Analyses of Metabolic Networks: Prototype Data Format for Describing Both Inter- and Intra-Metabolite Atom-level Connectivities", Proceedings for 5th International Conference on Systems Biology, 141-141 (2004)
8 Ohta, J., "Connectivity matrix method for analyses of biological networks and its application to atom-level analysis of a model network of carbohydrate metabolism", IEE Proceedings Systems Biology 153(5), 372-374 (2006)
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Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences
Okayama University Medical School
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