Summary: Extracting chemical features like Atom–Atom Mapping (AAM), Bond Changes (BCs) and Reaction Centres from biochemical reactions helps us understand the chemical composition of enzymatic reactions. Reaction Decoder is a robust command line tool, which performs this task with high accuracy. It supports standard chemical input/output exchange formats i.e. RXN/SMILES, computes AAM, highlights BCs and creates images of the mapped reaction. This aids in the analysis of metabolic pathways and the ability to perform comparative studies of chemical reactions based on these features.Availability and implementation: This software is implemented in Java, supported on Windows, Linux and Mac OSX, and freely available at https://github.com/asad/ReactionDecoderContact: asad@ebi.ac.uk or s9asad@gmail.com

Computer-Assisted Structure Elucidation (CASE) is of relevance for various fields in chemistry and biology such as natural products discovery or metabolomics. Here we report on several software components developed in our team over time which can form part of an integrated CASE package. We aim to design a user-friendly and flexible, yet powerful tool with Bioclipse [1] as the frontend. Bioclipse is an integrated software suite for chemo-and bioinformatics providing plug-ins for file handling and visualisation of compounds and spectra. Spectrum look-up and prediction is provided by our open NMR database NMRShiftDB [2], offering both 13C and 1H NMR prediction. We have recently demonstrated the prediction of proton NMR spectra based on NMRShiftDB data with an average error of 0.18 ppm [3]. The resulting CASE system will provide a choice of different structure generators, including stochastic search engines, based on Simulated Annealing and Genetic Algorithms.