Open Access<em>In silico</em> modeling of biochemical pathways
Author(s) -
Paolo Milazzo,
Roberta Gori,
Alessio Micheli,
Lucia Nasti,
Marco Podda
Publication year - 2021
Publication title -
biomedical science and engineering
Language(s) - English
Resource type - Journals
ISSN - 2531-9892
DOI - 10.4081/bse.2021.142
Subject(s) - in silico , ordinary differential equation , ode , computer science , biological system , dynamical systems theory , systems biology , statistical physics , computational biology , chemistry , mathematics , differential equation , physics , biology , mathematical analysis , biochemistry , quantum mechanics , gene
We present in silico modeling methods for the investigation of dynamical properties of biochemical pathways, that are chemical reaction networks underlying cell functioning. Since pathways are (complex) dynamical systems, in-silico models are often studied by applying numerical integration techniques for Ordinary Differential Equations (ODEs), or stochastic simulation algorithms. However, these techniques require a rather accurate knowledge of the kinetic parameters of the modeled chemical reactions. Moreover, in the case of very complex reaction networks, in silico analysis can become unfeasible from the computational viewpoint. Consequently, in the last few years several approaches have been proposed that focus on estimating or predicting dynamical properties from the analysis of the structure of the biochemical pathway. This means that the analysis focuses more on the interaction patterns than on the kinetic parameters, and this usually makes it possible to deduce the role of each molecule and how each molecule qualitatively influences each other, by abstracting away from quantitative details about concentrations and reaction rates.