On the Realisability of Chemical Pathways

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


Publikation: Kapitel i bog/rapport/konference-proceedingKonferencebidrag i proceedingsForskningpeer review


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.

TitelBioinformatics Research and Applications - 19th International Symposium, ISBRA 2023, Proceedings
RedaktørerXuan Guo, Serghei Mangul, Murray Patterson, Alexander Zelikovsky
ForlagSpringer Science+Business Media
ISBN (Trykt)9789819970735
StatusUdgivet - 2023
Begivenhed19th International Symposium on Bioinformatics Research and Applications, ISBRA 2023 - Wroclaw, Polen
Varighed: 9. okt. 202312. okt. 2023


Konference19th International Symposium on Bioinformatics Research and Applications, ISBRA 2023
NavnLecture Notes in Computer Science

Bibliografisk note

Funding Information:
This work is supported by the Novo Nordisk Foundation grant NNF19OC0057834 and by the Independent Research Fund Denmark, Natural Sciences, grant DFF-0135-00420B.


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