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Bioinformatics. 2016 Jul 1;32(13):2065-6. doi: 10.1093/bioinformatics/btw096. Epub 2016 Feb 22.

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

Author information

1
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.
2
European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
3
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.
4
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.
5
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.
6
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.
7
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.

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.

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.

PMID:
27153692
PMCID:
PMC4920114
DOI:
10.1093/bioinformatics/btw096
[Indexed for MEDLINE]
Free PMC Article

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