title: Reaction Decoder Tool (RDT): extracting features from chemical reactions.
abstract: 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.
  
  
  
  This software is implemented in Java, supported on Windows, Linux and Mac OSX, and freely available at https://github.com/asad/ReactionDecoder
  
  
  
  : asad@ebi.ac.uk or s9asad@gmail.com.
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Congenica Ltd, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Syed Asad
authors.initials: SA
authors.lastname: Rahman
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Gilliean
authors.initials: G
authors.lastname: Torrance
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK DISI, University of Bologna, V.Le Risorgimento 2, Bologna, Italy.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Baldacci
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
authors.forename: Sergio
authors.initials: S
authors.lastname: Martínez Cuesta
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Michael Smith Laboratories, the University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
authors.forename: Franz
authors.initials: F
authors.lastname: Fenninger
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Nimish
authors.initials: N
authors.lastname: Gopal
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Saket
authors.initials: S
authors.lastname: Choudhary
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Innovation Centre (Unit 23), Cambridge Science Park, NextMove Software Ltd, Cambridge CB4 0EY, UK.
authors.forename: John W
authors.initials: JW
authors.lastname: May
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Bioengineering, UCSF School of Pharmacy, San Francisco, CA 94158, USA.
authors.forename: Gemma L
authors.initials: GL
authors.lastname: Holliday
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Christoph
authors.initials: C
authors.lastname: Steinbeck
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Janet M
authors.initials: JM
authors.lastname: Thornton
mesh_terms: D001671:Biochemistry / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining; D062126:Databases, Chemical; D053858:Metabolic Networks and Pathways; D012984:Software