Metabolic Pathway Builder: Connecting, completing and exploring biochemical and genomic data
The knowledge on the connections between the genome, the proteome and the metabolome of an organism is a key to a global understanding of the dynamics of its cells: the metabolic reactions, which produce energy and transform small molecules necessary for the cell to operate, are catalyzed by enzymes, which, as proteins, are synthesized according to the information coded in the genes. Metabolic Pathway Builder (MPB) has been designed to help biologists annotating genomic sequences, i.e. identifying the coding sequences and characterizing the proteins they code for. Some of these proteins are enzymes and MPB provides methods for predicting the metabolic reactions they catalyze. MPB makes use of the ChemAxon library for managing and displaying chemical compounds and metabolic reactions. In MPB, the links between genes, proteins and reactions are indeed modeled in a large entity - relationship network that can be browsed and queried. For instance, in the context of spectrometry analysis, a powerful query relies on the structural search facility of JChem Base. It retrieves all the metabolites which share a chemical substructure; the metabolic reactions and pathways which involve these metabolites can be further identified and displayed by MPB, together with the genes the products of which catalyze the reactions of the pathways. Integrating other functions provided by the ChemAxon library will allow Metabolic Pathway Builder to extend its capacities further in the direction of chemoinformatics. Genostar is particularly interested in increasing the connections between its software modules and external biochemical and chemical databases, and the 3D-visualization capabilities.