ReactionCode: Format for Reaction Searching, Analysis, Classification, Transform, and Encoding/Decoding

Abstract

In the past two decades a lot of different formats for molecules and reactions have been created. These formats were mostly developed for the purposes of identifiers, representation, classification, analysis and data exchange. A lot of efforts have been made on molecule formats but only few for reactions where the endeavors have been made mostly by companies leading to proprietary formats. Here, we developed a new open-source format which allows to encode and decode a reaction into multi-layers machine readable code, which aggregates reactants and products into a condensed graph of reaction (CGR). This format is flexible and can be used in a context of reaction similarity searching and classification. It is also designed for database organization, machine learning applications and as a new transform reaction language.

Proposal of the Annotation of Phosphorylated Amino Acids and Peptides Using Biological and Chemical Codes

“…1 to the oxygen atom, considering a sugar molecule as a heterocyclic compound. The INChI code [ 21 ] and the ReactionCode [ 60 ] also contain unambiguous numbering of atoms in a molecule. The rules of atom numbering proposed below seem to be more intuitive than these used in the above codes.…”