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Updated: May 29, 2025
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A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
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Pathway Realizability in Chemical Networks
Jakob L Andersen1, Sissel Banke1, Rolf Fagerberg1
1Department of Mathematics and Computer Science, University of Southern Denmark, Odense M, Denmark.
Summary
This study introduces a method to determine if chemical pathways are executable, providing a reaction sequence for realizable pathways. It enhances pathway analysis by addressing the missing link of practical execution in chemical contexts.
Area of Science:
- Biochemistry and Systems Biology
- Computational Chemistry
- Chemical Engineering
Background:
- Pathway analysis is crucial in chemistry, but existing frameworks lack methods to assess the practical execution of identified pathways.
- Determining pathway realizability is essential for understanding and manipulating biochemical and chemical processes.
Purpose of the Study:
- To develop a method for analyzing the realizability of chemical pathways.
- To provide a computational framework for assessing if a sequence of reactions can be practically executed.
- To extend the concept of pathway realizability and its implications.
Main Methods:
- Utilizing Petri net reachability analysis to determine pathway execution feasibility.
- Developing a certificate generation method to encode reaction sequences for realizable pathways.
- Applying the framework to the pentose phosphate pathway for empirical validation.
Main Results:
- A novel method for analyzing pathway realizability based on Petri nets has been established.
- The method successfully identifies realizable pathways and provides a valid reaction sequence.
- Extended notions of realizability, including network catalysts, were explored and exemplified.
Conclusions:
- The developed method provides a robust approach to assess and confirm the practical execution of chemical pathways.
- This work lays the foundation for a mathematical theory of pathway realizability, impacting computational chemistry and systems biology.
- Understanding pathway execution is vital for interpreting implicit choices in pathway depictions and advancing chemical process design.
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