Network cheminformatics: gap filling and identifying new reactions in metabolic networks based on metabolite similarity
by Neil Swainston, Experimental Officer at Manchester Centre for Integrative Systems Biology on Aug 29, 2011
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The number of published metabolic network reconstructions are increasing, as are their applications. However, such reconstructions commonly include gaps (see Figure 1), which are due to incomplete ...
The number of published metabolic network reconstructions are increasing, as are their applications. However, such reconstructions commonly include gaps (see Figure 1), which are due to incomplete source databases or holes in biochemical knowledge reported in literature. The filling of such gaps has been aided through automated techniques which attempt to mitigate these gaps by adding reactions from external resources such as KEGG.
The approach introduced here is to apply cheminformatics to determine and quantify chemical similarity across all metabolites in a metabolic network of S. cerevisiae. The hypothesis is that those metabolite pairs of high chemical similarity are likely to form reaction pairs, in which one metabolite can be converted to the other by a single chemical reaction. The similar scoring pairs that do not currently form a reaction pair in the network can be analysed, by either comparison with existing data resources or by literature searches, to determine whether they take part in a metabolic reaction.
Following this approach, preliminary results have led to the discovery of missing information from KEGG, and the assignment of function and determination of kinetic constants to a gene of previously unknown function.
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