MetExplore stores metabolic networks into a relational database (freely available on demand). Information about metabolic networks currently come from BioCyc-like databases. We also included in MetExplore the information about metabolites stored in Metabolome.jp.

Various filters can be applied in MetExplore to restrict the scope of the study, for example by selecting only particular pathways or by restricting the network to the small-molecule metabolism. MetExplore also allows filtering of currency metabolites, cofactors or generic reactions, often sources of misinterpretations in metabolic graph analysis and which also bring significant quantities of noise to the derived networks.

MetExplore provides several functions that can be applied on filtered metabolic networks. MetExplore is thus able to deal with data from metabolomics experiments by mapping a list of masses or identifiers onto filtered metabolic networks. MetExplore also provides several functions based on the modelling of the metabolic network by a graph model. Two functions are dedicated to the identification of "weak" points in the metabolic network to help the design of new drugs.

MetExplore allows to display information about the whole sets of metabolites present in a filtered metabolic network. Apart from classical information such as mass, formula, reactions and pathways where each metabolite is involved, MetExplore displays also the topological properties of the metabolite in the filtered metabolic network.

At last, the MetExplore user can export a filtered metabolic network into several graph models (compound graph, reaction graph or bipartite graph). One can also upload his own SBML file and export it in graph models.