Fig. 1: ATLAS workflow applied to known biological and bioactive compounds.
From: Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx
1. Unification- collection of metabolic reactions and biochemical compounds from different publicly available databases, which were merged into a consistent and duplicate-free database, called bioDB. 2. Curation- compounds were annotated with molecular identifiers and reactions were annotated with reaction mechanisms. 3. Expansion- generalized reaction rules from BNICE.ch were applied to bioDB compounds to generate all possible reactions producing known biological or chemical products. 4. Analysis- the connectivity of the biochemical reaction networks was analyzed before and after reaction prediction, as well as the integration of compounds not previously connected in known biochemical networks. 5. Distribution- the results were made available online (https://lcsb-databases.epfl.ch/Atlas2). ΔfGʹ°: estimated Gibbs free energy of formation for compounds under biological conditions.
