On the Realisability of Chemical Pathways

Jakob L. Andersen, Sissel Banke*, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

Abstract

The exploration of pathways and alternative pathways that have a specific function is of interest in numerous chemical contexts. A framework for specifying and searching for pathways has previously been developed, but a focus on which of the many pathway solutions are realisable, or can be made realisable, is missing. Realisable here means that there actually exists some sequencing of the reactions of the pathway that will execute the pathway. We present a method for analysing the realisability of pathways based on the reachability question in Petri nets. For realisable pathways, our method also provides a certificate encoding an order of the reactions which realises the pathway. We present two extended notions of realisability of pathways, one of which is related to the concept of network catalysts. We exemplify our findings on the pentose phosphate pathway. Lastly, we discuss the relevance of our concepts for elucidating the choices often implicitly made when depicting pathways.

Original languageEnglish
Title of host publicationBioinformatics Research and Applications - 19th International Symposium, ISBRA 2023, Proceedings
EditorsXuan Guo, Serghei Mangul, Murray Patterson, Alexander Zelikovsky
PublisherSpringer Science+Business Media
Publication date2023
Pages409-419
ISBN (Print)9789819970735
DOIs
Publication statusPublished - 2023
Event19th International Symposium on Bioinformatics Research and Applications, ISBRA 2023 - Wroclaw, Poland
Duration: 9. Oct 202312. Oct 2023

Conference

Conference19th International Symposium on Bioinformatics Research and Applications, ISBRA 2023
Country/TerritoryPoland
CityWroclaw
Period09/10/202312/10/2023
SeriesLecture Notes in Computer Science
Volume14248
ISSN0302-9743

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