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

Syed Asad Rahman, Gilliean Torrance, Lorenzo Baldacci, Sergio Martínez Cuesta, Franz Fenninger, Nimish Gopal, Saket Choudhary, John W. May, Gemma L. Holliday, Christoph Steinbeck, Janet M. Thornton
2016 Bioinformatics  
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
more » ... 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
doi:10.1093/bioinformatics/btw096 pmid:27153692 pmcid:PMC4920114 fatcat:dkglyqt6zzaw7mrtk2ylndhfvq