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arXiv · 1604.06379

Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions

Christoph Flamm·Daniel Merkle·Peter F. Stadler·Uffe Thorsen
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Abstract

Graph transformation systems have the potential to be realistic models of chemistry, provided a comprehensive collection of reaction rules can be extracted from the body of chemical knowledge. A first key step for rule learning is the computation of atom-atom mappings, i.e., the atom-wise correspondence between products and educts of all published chemical reactions. This can be phrased as a maximum common edge subgraph problem with the constraint that transition states must have cyclic structure. We describe a search tree method well suited for small edit distance and an integer linear program best suited for general instances and demonstrate that it is feasible to compute atom-atom maps at large scales using a manually curated database of biochemical reactions as an example. In this context we address the network completion problem.

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Christoph Flamm, Daniel Merkle, Peter F. Stadler, Uffe Thorsen. 2016-04-21. Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions. https://arxiv.org/abs/1604.06379

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