Metabolic pathway prediction based on inclusive relation between cyclic substructures

Abstract

Secondary metabolites are highly species-specific and play important roles in the survival of the producing organism within its natural habitat. Systematization of secondary metabolic pathways is necessary to understand species-specific metabolic pathways and to develop new drugs, etc. To attain this, we have made a database system called KNApSAcK, which describes the relationships between metabolites and species. On March 21, 2009, KNApSAcK had 34,852 metabolite entries and 68,819 metabolite-species pair entries. Though the chemical structures of around 50,000 secondary metabolites are known, information on their pathways is very limited. In this work, we have developed an algorithm to predict metabolic pathways on the basis of chemical structures of metabolites by exploiting the information contained in their cyclic substructures. Also, to handle a huge amount of these metabolites and to predict metabolic pathways automatically, we have developed a software tool called MetClassifier. MetClassifier is written in C and uses the OpenGL, GLUT (http://www.opengl.org/resources/libraries/glut/) and AntTweakBar (http://www.antisphere.com/Wiki/tools:anttweakbar) libraries. MetClassifier can be downloaded from the following URL (http://kanaya.naist.jp/MetClassifier/). © 2009 The Japanese Society for Plant Cell and Molecular Biology.