Finding relevant biotransformation routes in weighted metabolic networks using atom mapping rules

Abstract

Computational analysis of pathways in metabolic networks has numerous applications in systems biology. While graph theory-based approaches have been pre- sented that find biotransformation routes from one metabolite to another in these net- works, most of these approaches suffer from finding too many routes, most of which are biologically infeasible or meaningless. We present a novel approach for finding relevant routes based on atom mapping rules (describing which educt atoms are mapped onto which product atoms in a chemical reaction). This leads to a reformulation of the problem as a lightest path search in a degree-weighted metabolic network. A key component of the approach is a new method of computing optimal atom mapping rules.