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2023 | OriginalPaper | Buchkapitel

On the Realisability of Chemical Pathways

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

Erschienen in: Bioinformatics Research and Applications

Verlag: Springer Nature Singapore

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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.

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Vorheriges Kapitel DCNN: Dual-Level Collaborative Neural Network for Imbalanced Heart Anomaly Detection

Nächstes Kapitel A Brief Study of Gene Co-expression Thresholding Algorithms

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Titel: On the Realisability of Chemical Pathways
verfasst von: Jakob L. Andersen
Sissel Banke
Rolf Fagerberg
Christoph Flamm
Daniel Merkle
Peter F. Stadler
Verlag: Springer Nature Singapore
Buch: Bioinformatics Research and Applications
Print ISBN: 978-981-9970-73-5

Electronic ISBN: 978-981-9970-74-2

Copyright-Jahr: 2023
DOI: https://doi.org/10.1007/978-981-99-7074-2_32

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