A Constraint Based Method for Optimization in Metabolic Pathways

  • Mouli Das
  • Subhasis Mukhopadhyay
  • Rajat K. De
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5909)

Abstract

The analysis of pathways in metabolic networks has become an important approach for understanding metabolic systems. Constraint-based approaches recently brought new insight into our understanding of metabolism. Here we introduce a method for identifying optimal metabolic pathways. The method, generates data on reaction fluxes based on biomass conservation constraint and formulates constraints incorporating weighting coefficients corresponding to concentration of enzymes catalyzing the reactions. The effectiveness of the present method is demonstrated on the pentose phosphate pathway (PPP) in T. cruzi and on a large network of the plant polyamine pathway existing in the literature. A comparative study with the existing extreme pathway analysis (EPA) also forms a part of this investigation.

Keywords

FBA stoichiometric matrix polyamine pathway 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Mouli Das
    • 1
  • Subhasis Mukhopadhyay
    • 2
  • Rajat K. De
    • 1
  1. 1.Machine Intelligence UnitIndian Statistical InstituteKolkataIndia
  2. 2.Department of Bio-Physics, Molecular Biology and BioinformaticsCalcutta UniversityKolkataIndia

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