2012/08/15 by Jakob L. Andersen, Christoph Flamm, Andersen, Jakob L. +5 · 3 citations
Computer Science · #Advanced Software Engineering Methodologies #Computational Engineering #Discrete Mathematics (cs.DM) #FOS: Biological sciences #FOS: Computer and information sciences #Finance #Model-Driven Software Engineering Techniques #Molecular Networks (q-bio.MN) #Semantic Web and Ontologies #Software Engineering Research #and Science (cs.CE)
paper · pdf · doi:10.48550/arxiv.1208.3153
openalex publication_date 2012/08/15 · openalex created_date 2025/10/24 · openalex updated_date 2026/07/28
Modeling molecules as undirected graphs and chemical reactions as graph\nrewriting operations is a natural and convenient approach tom odeling\nchemistry. Graph grammar rules are most naturally employed to model elementary\nreactions like merging, splitting, and isomerisation of molecules. It is often\nconvenient, in particular in the analysis of larger systems, to summarize\nseveral subsequent reactions into a single composite chemical reaction. We use\na generic approach for composing graph grammar rules to define a chemically\nuseful rule compositions. We iteratively apply these rule compositions to\nelementary transformations in order to automatically infer complex\ntransformation patterns. This is useful for instance to understand the net\neffect of complex catalytic cycles such as the Formose reaction. The\nautomatically inferred graph grammar rule is a generic representative that also\ncovers the overall reaction pattern of the Formose cycle, namely two carbonyl\ngroups that can react with a bound glycolaldehyde to a second glycolaldehyde.\nRule composition also can be used to study polymerization reactions as well as\nmore complicated iterative reaction schemes. Terpenes and the polyketides, for\ninstance, form two naturally occurring classes of compounds of utmost\npharmaceutical interest that can be understood as "generalized polymers"\nconsisting of five-carbon (isoprene) and two-carbon units, respectively.\n