Computer Research and Modeling
RUS  ENG    JOURNALS   PEOPLE   ORGANISATIONS   CONFERENCES   SEMINARS   VIDEO LIBRARY   PACKAGE AMSBIB  
General information
Latest issue
Archive

Search papers
Search references

RSS
Latest issue
Current issues
Archive issues
What is RSS



Computer Research and Modeling:
Year:
Volume:
Issue:
Page:
Find






Personal entry:
Login:
Password:
Save password
Enter
Forgotten password?
Register


Computer Research and Modeling, 2015, Volume 7, Issue 6, Pages 1241–1267
DOI: https://doi.org/10.20537/2076-7633-2015-7-6-1241-1267
(Mi crm291)
 

This article is cited in 2 scientific papers (total in 2 papers)

ANALYSIS AND MODELING OF COMPLEX LIVING SYSTEMS

Stoichiometric synthesis of metabolic pathways

I. G. Minkevich

G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
Full-text PDF (757 kB) Citations (2)
References:
Abstract: A vector-matrix approach to the theoretical design of metabolic pathways converting chemical compounds, viz., preset substrates, into desirable products is described. It is a mathematical basis for computer-aided generation of alternative biochemical reaction sets executing the given substrate-product conversion. The pathways are retrieved from the used database of biochemical reacions and utilize the reaction stoichiometry and restrictions based on the irreversibility of a part of them. Particular attention is paid to the analysis of restriction interrelations. It is shown that the number of restrictions can be notably reduced due to the existence of families of parallel restricting planes in the space of reaction flows. Coinciding planes of contradirectional restrictions result in the existence of fixed reaction flow values. The problem of exclusion of so called futile cycles is also considered. Utilization of these factors allows essential lowering of the problem complexity and necessary computational resources. An example of alternative biochemical pathway computation for conversion of glucose and glycerol into succinic acid is given. It is found that for a preset “substrate-product”; pair many pathways have the same high-energy bond balance.
Keywords: theoretical biochemistry, substrate, product, conversion, alternative metabolic pathways, stoichiometry, vector-matrix description, irreversible reactions, families of restrictions.
Received: 29.10.2015
Document Type: Article
UDC: 519.8
Language: English
Citation: I. G. Minkevich, “Stoichiometric synthesis of metabolic pathways”, Computer Research and Modeling, 7:6 (2015), 1241–1267
Citation in format AMSBIB
\Bibitem{Min15}
\by I.~G.~Minkevich
\paper Stoichiometric synthesis of metabolic pathways
\jour Computer Research and Modeling
\yr 2015
\vol 7
\issue 6
\pages 1241--1267
\mathnet{http://mi.mathnet.ru/crm291}
\crossref{https://doi.org/10.20537/2076-7633-2015-7-6-1241-1267}
Linking options:
  • https://www.mathnet.ru/eng/crm291
  • https://www.mathnet.ru/eng/crm/v7/i6/p1241
  • This publication is cited in the following 2 articles:
    Citing articles in Google Scholar: Russian citations, English citations
    Related articles in Google Scholar: Russian articles, English articles
    Computer Research and Modeling
    Statistics & downloads:
    Abstract page:122
    Full-text PDF :44
    References:39
     
      Contact us:
     Terms of Use  Registration to the website  Logotypes © Steklov Mathematical Institute RAS, 2024