Abstract
Metabolic pathway analysis is one of the tools used in biology and medicine in order to understand reaction cycles in living cells. A shortcoming of the approach, however, is that reactions are analysed only at a level corresponding to what is known as the ’collective token view’ in Petri nets, i.e., summarising the number of atoms of certain types in a compound, but not keeping track of their identity.
In this paper we propose a refinement of pathway analysis based on hypergraph grammars, modelling reactions at a molecular level. We consider as an example the citric acid cycle, a classical, but non-trivial reaction for energy utilisation in living cells. Our approach allows the molecular analysis of the cycle, tracing the flow of individual carbon atoms based on a simulation using the graph transformation tool AGG.
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Ehrig, K., Heckel, R., Lajios, G. (2006). Molecular Analysis of Metabolic Pathway with Graph Transformation. In: Corradini, A., Ehrig, H., Montanari, U., Ribeiro, L., Rozenberg, G. (eds) Graph Transformations. ICGT 2006. Lecture Notes in Computer Science, vol 4178. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11841883_9
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DOI: https://doi.org/10.1007/11841883_9
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