Reaction Decoder Tool (RDT): extracting features from chemical reactions

Syed Asad Rahman(European Bioinformatics Institute), Gilliean Torrance(European Bioinformatics Institute), Lorenzo Baldacci(European Bioinformatics Institute), Sergio Martínez Cuesta(European Bioinformatics Institute), Franz Fenninger(European Bioinformatics Institute), Nimish Gopal(European Bioinformatics Institute), Saket Choudhary(European Bioinformatics Institute), John W. May(European Bioinformatics Institute), Gemma L. Holliday(European Bioinformatics Institute), Christoph Steinbeck(European Bioinformatics Institute), Janet M. Thornton(European Bioinformatics Institute)
Bioinformatics
February 22, 2016
10.1093/bioinformatics/btw096
Cited by 107Open Access
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Abstract

Abstract 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/ReactionDecoder Contact: asad@ebi.ac.uk or s9asad@gmail.com

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