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Metabolic Networks: Beyond the Graph

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Drugs are devised to enter into the metabolism of an organism in order to produce a desired effect. From the chemical point of view, cellular metabolism is constituted by a complex network of reactions transforming metabolites one in each other. Knowledge on the structure of this network could help to develop novel methods for drug design, and to comprehend the root of known unexpected side effects. Many large-scale studies on the structure of metabolic networks have been developed following models based on different kinds of graphs as the fundamental image of the reaction network. Graphs models, however, comport wrong assumptions regarding the structure of reaction networks that may lead into wrong conclusions if they are not taken into account. In this article we critically review some graph-theoretical approaches to the analysis of centrality, vulnerability and modularity of metabolic networks, analyzing their limitations in estimating these key network properties, consider some proposals explicit or implicitly based on directed hypergraphs regarding their ability to overcome these issues, and review some recent implementation improvements that make the application of these models in increasingly large networks a viable option.

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Keywords: Metabolic networks; centrality measures; directed hypergraphs; drug design; flux balance analysis; graph models; metabolites; modularity; reaction networks; vulnerability

Document Type: Research Article

Publication date: June 1, 2011

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  • Current Computer-Aided Drug Design aims to publish all the latest developments in drug design based on computational techniques. The field of computer-aided drug design has had extensive impact in the area of drug design. Current Computer-Aided Drug Design is an essential journal for all medicinal chemists who wish to be kept informed and up-to-date with all the latest and important developments in computer-aided methodologies and their applications in drug discovery. Each issue contains a series of timely, in-depth reviews written by leaders in the field, covering a range of computational techniques for drug design, screening, ADME studies, etc., providing excellent rationales for drug development.
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