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.
|Bioinformatics Research and Applications - 19th International Symposium, ISBRA 2023, Proceedings
|Xuan Guo, Serghei Mangul, Murray Patterson, Alexander Zelikovsky
|Springer Science+Business Media
|Udgivet - 2023
|19th International Symposium on Bioinformatics Research and Applications, ISBRA 2023 - Wroclaw, Polen
Varighed: 9. okt. 2023 → 12. okt. 2023
|19th International Symposium on Bioinformatics Research and Applications, ISBRA 2023
|09/10/2023 → 12/10/2023
|Lecture Notes in Computer Science
Bibliografisk noteFunding 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.