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Reaction Decoder

Atom-Atom Mapping (AAM), Reaction Similarity Tool

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Reaction Decoder Tool (EC-BLAST)

Author: Syed Asad Rahman
c/o EMBL-European BioInformatics Institute (EBI)
WTGC, CB10 1SD Hinxton

Note: The copyright of this software belongs to the author and the EMBL-European BioInformatics Institute (EBI).

Reference: Rahman, S.A. EC-BLAST: A Tool to Automatically Search and Compare Enzyme Reactions, Nature Methods.

"Reaction Decoder" Tool:

a) Can extract reaction transformation patterns,
b) Perform atom-atom mapping and
c) Compare reaction pairs and report its similarity metrics.

Note: This code is compatible to JVM 7.0+

Reaction Decoder Web Site


  • Atom-Atom Mapping on a chemically balanced reaction.
  • Compute Reaction Similarity as reported by EC-BLAST.
  • Generate reaction patterns and bond change fingerprints.
  • RXN as input/output format and PNG for the mapped reaction.
  • SMILES as input and output.
  • Build on the Small Molecule Subgraph Detector (SMSD)
  • and Chemistry Development Kit (CDK).

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