Atom Tracking Using Cayley Graphs

Marc Hellmuth, Daniel Merkle, Nikolai Nøjgaard*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

Abstract

While atom tracking with isotope-labeled compounds is an essential and sophisticated wet-lab tool in order to, e.g., illuminate reaction mechanisms, there exists only a limited amount of formal methods to approach the problem. Specifically when large (bio-)chemical networks are considered where reactions are stereo-specific, rigorous techniques are inevitable. We present an approach using the right Cayley graph of a monoid in order to track atoms concurrently through sequences of reactions and predict their potential location in product molecules. This can not only be used to systematically build hypothesis or reject reaction mechanisms (we will use the mechanism “Addition of the Nucleophile, Ring Opening, and Ring Closure” as an example), but also to infer naturally occurring subsystems of (bio-)chemical systems. We will exemplify the latter by analysing the carbon traces within the TCA cycle and infer subsystems based on projections of the right Cayley graph onto a set of relevant atoms.

Original languageEnglish
Title of host publicationProceedings of Bioinformatics Research and Applications : 16th International Symposium, ISBRA 2020
EditorsZhipeng Cai, Ion Mandoiu, Giri Narasimhan, Pavel Skums, Xuan Guo
PublisherSpringer
Publication date2020
Pages406-415
ISBN (Print)9783030578206
DOIs
Publication statusPublished - 2020
Event16th International Symposium on Bioinformatics Research and Applications, ISBRA 2020 - Moscow, Russian Federation
Duration: 1. Dec 20204. Dec 2020

Conference

Conference16th International Symposium on Bioinformatics Research and Applications, ISBRA 2020
CountryRussian Federation
CityMoscow
Period01/12/202004/12/2020
SeriesLecture Notes in Computer Science
Number12304
ISSN0302-9743

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