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A Web Tool for Generating High Quality Machine-readable Biological Pathways
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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.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|February 3, 2025
PubMed
Summary
This summary is machine-generated.

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.

Keywords:
Petri netchemical reaction networkcheminformaticsdirected multi-hypergraphpentose phosphate pathway

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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.