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An algorithm for rapid computational construction of metabolic networks: A cholesterol biosynthesis example

Aleš Belič, Denis Pompon, Katalin Monostory, Diane Kelly, Steven Kelly Orcid Logo, Damjana Rozman

Computers in Biology and Medicine, Volume: 43, Issue: 5, Pages: 471 - 480

Swansea University Authors: Diane Kelly, Steven Kelly Orcid Logo

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DOI (Published version): 10.1016/j.compbiomed.2013.02.017

Abstract

Alternative pathways of metabolic networks represent the escape routes that can reduce drug efficacyand can cause severe adverse effects. In this paper we introduce a mathematical algorithm and a codingsystem for rapid computational construction of metabolic networks.The initial data for the algorit...

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Published in: Computers in Biology and Medicine
ISSN: 0010-4825
Published: Elsevier BV 2013
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URI: https://cronfa.swan.ac.uk/Record/cronfa15174
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first_indexed 2013-07-23T12:13:57Z
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spelling 2021-10-29T09:32:32.2360252 v2 15174 2013-07-08 An algorithm for rapid computational construction of metabolic networks: A cholesterol biosynthesis example 5ccf81e5d5beedf32ef8d7c3d7ac6c8c Diane Kelly Diane Kelly true false b17cebaf09b4d737b9378a3581e3de93 0000-0001-7991-5040 Steven Kelly Steven Kelly true false 2013-07-08 SGMED Alternative pathways of metabolic networks represent the escape routes that can reduce drug efficacyand can cause severe adverse effects. In this paper we introduce a mathematical algorithm and a codingsystem for rapid computational construction of metabolic networks.The initial data for the algorithmare the source substrate code and the enzyme/metabolite interaction tables.The major strength of thealgorithm is the adaptive coding system of the enzyme–substrate interactions. A reverse application ofthe algorithm is also possible,when optimisation algorithm is used to compute the enzyme/metaboliterules from the reference network structure.The coding system is user-defined and must be adapted tothe studied problem.The algorithm is most effective for computation of networks that consist ofmetabolites with similar molecular structures.The computation of the cholesterol biosynthesismetabolic network suggests that 89 intermediates can theoretically be formed between lanosteroland cholesterol,only 20 are presently considered as cholesterol intermediates.Alternative metabolitesmay represent links with other metabolic networks both as precursors and metabolites ofcholesterol. Apossible cholesterol-by-pass pathway to bile acids metabolism through cholestanol is suggested. Journal Article Computers in Biology and Medicine 43 5 471 480 Elsevier BV 0010-4825 Systems biology, binary coding, modelling, simulation, metabolic networks 1 6 2013 2013-06-01 10.1016/j.compbiomed.2013.02.017 http://dx.doi.org/10.1016/j.compbiomed.2013.02.017 COLLEGE NANME Medical School - School COLLEGE CODE SGMED Swansea University 2021-10-29T09:32:32.2360252 2013-07-08T13:00:46.2918205 Faculty of Medicine, Health and Life Sciences Swansea University Medical School - Medicine Aleš Belič 1 Denis Pompon 2 Katalin Monostory 3 Diane Kelly 4 Steven Kelly 0000-0001-7991-5040 5 Damjana Rozman 6
title An algorithm for rapid computational construction of metabolic networks: A cholesterol biosynthesis example
spellingShingle An algorithm for rapid computational construction of metabolic networks: A cholesterol biosynthesis example
Diane Kelly
Steven Kelly
title_short An algorithm for rapid computational construction of metabolic networks: A cholesterol biosynthesis example
title_full An algorithm for rapid computational construction of metabolic networks: A cholesterol biosynthesis example
title_fullStr An algorithm for rapid computational construction of metabolic networks: A cholesterol biosynthesis example
title_full_unstemmed An algorithm for rapid computational construction of metabolic networks: A cholesterol biosynthesis example
title_sort An algorithm for rapid computational construction of metabolic networks: A cholesterol biosynthesis example
author_id_str_mv 5ccf81e5d5beedf32ef8d7c3d7ac6c8c
b17cebaf09b4d737b9378a3581e3de93
author_id_fullname_str_mv 5ccf81e5d5beedf32ef8d7c3d7ac6c8c_***_Diane Kelly
b17cebaf09b4d737b9378a3581e3de93_***_Steven Kelly
author Diane Kelly
Steven Kelly
author2 Aleš Belič
Denis Pompon
Katalin Monostory
Diane Kelly
Steven Kelly
Damjana Rozman
format Journal article
container_title Computers in Biology and Medicine
container_volume 43
container_issue 5
container_start_page 471
publishDate 2013
institution Swansea University
issn 0010-4825
doi_str_mv 10.1016/j.compbiomed.2013.02.017
publisher Elsevier BV
college_str Faculty of Medicine, Health and Life Sciences
hierarchytype
hierarchy_top_id facultyofmedicinehealthandlifesciences
hierarchy_top_title Faculty of Medicine, Health and Life Sciences
hierarchy_parent_id facultyofmedicinehealthandlifesciences
hierarchy_parent_title Faculty of Medicine, Health and Life Sciences
department_str Swansea University Medical School - Medicine{{{_:::_}}}Faculty of Medicine, Health and Life Sciences{{{_:::_}}}Swansea University Medical School - Medicine
url http://dx.doi.org/10.1016/j.compbiomed.2013.02.017
document_store_str 0
active_str 0
description Alternative pathways of metabolic networks represent the escape routes that can reduce drug efficacyand can cause severe adverse effects. In this paper we introduce a mathematical algorithm and a codingsystem for rapid computational construction of metabolic networks.The initial data for the algorithmare the source substrate code and the enzyme/metabolite interaction tables.The major strength of thealgorithm is the adaptive coding system of the enzyme–substrate interactions. A reverse application ofthe algorithm is also possible,when optimisation algorithm is used to compute the enzyme/metaboliterules from the reference network structure.The coding system is user-defined and must be adapted tothe studied problem.The algorithm is most effective for computation of networks that consist ofmetabolites with similar molecular structures.The computation of the cholesterol biosynthesismetabolic network suggests that 89 intermediates can theoretically be formed between lanosteroland cholesterol,only 20 are presently considered as cholesterol intermediates.Alternative metabolitesmay represent links with other metabolic networks both as precursors and metabolites ofcholesterol. Apossible cholesterol-by-pass pathway to bile acids metabolism through cholestanol is suggested.
published_date 2013-06-01T03:17:17Z
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score 11.014067

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