ReactionCode: format for reaction searching, analysis, classification, transform, and encoding/decoding

Delannée, Victorien; Nicklaus, Marc C.

doi:10.1186/s13321-020-00476-x

“…Intermediate structures are often used to describe reaction mechanisms such as in textbook presentations of a nucleophile substitution: Similar to these intermediate structures of a reaction mechanism there are Imaginary Transition Structures (ITS) [15] or Condensed Graphs of Reaction (CGR) [16], [17] that conceptualize a chemical reaction as one single pseudo molecule with incoming bonds and outgoing bonds. Delannée and Nicklaus have used this idea to create a novel reaction representation "ReactionCode" [18], which is a hierarchical code beginning from the reaction center and then continuing out from there. These presentations of reactions are alternatives to the arrow notation and have lots of benefits [19].…”

Section: Reaction Center Expressed In R-splmentioning

confidence: 99%

Reaction SPL - extension of a public document markup standard to chemical reactions

Schadow

¹

,

Borodina

²

,

Delannée³

et al. 2022

Preprint

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There are numerous formats and data models for describing reaction-related data. However, each offers only a limited coverage of the multitude of information that can be of interest to a broad user base in the context of chemical reactions. Structured Product Labeling (SPL) is a robust yet fairly light public XML document standard. It uses a highly generic but usefully refinable data schema, which is, like a language, highly expressive. We are therefore presenting an extension of SPL to chemical reactions (“Reaction SPL”). This extension is designed to support chemical manufacturing processes, which include as a minimum the chemical reaction and the procedures and conditions to run it. We provide an overview of the SPL reaction specification structures followed by some examples of documents with reaction data: predicted single-step reactions, a two-step synthesis, an enzymatic reaction, an example how to represent a reaction center, a patent, and a fully annotated reaction with by-products. Special attention is given to a mechanism for atom-atom mapping of reactions as well as to the possibility to integrate Reaction SPL with laboratory automation equipment, in particular automated synthesis devices.

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“…Similar to these intermediate structures of a reaction mechanism, there are Imaginary Transition Structures (ITS) [ 21 ] or Condensed Graphs of Reaction (CGR) [ 22 , 23 ] that conceptualize a chemical reaction as one single pseudo- molecule with incoming bonds and outgoing bonds. Delannée and Nicklaus have used this idea to create a novel reaction representation “ReactionCode” [ 24 ], which is a hierarchical code beginning from the reaction center and then continuing out from there. These presentations of reactions are alternatives to the arrow notation and have lots of benefits [ 25 ].…”

Section: Types Of Possible Reaction Spl Documents and Examplesmentioning

confidence: 99%

Reaction SPL – extension of a public document markup standard to chemical reactions

Schadow¹,

Borodina

²

,

Delannée

³

et al. 2022

Pure and Applied Chemistry

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0

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There are numerous formats and data models for describing reaction-related data. However, each offers only a limited coverage of the multitude of information that can be of interest to a broad user base in the context of chemical reactions. Structured Product Labeling (SPL) is a robust yet fairly light public XML document standard. It uses a highly generic but usefully refinable data schema, which is, like a language, highly expressive. We are therefore presenting an extension of SPL to chemical reactions (“Reaction SPL”). This extension is designed to support chemical manufacturing processes, which include as a minimum the chemical reaction and the procedures and conditions to run it. We provide an overview of the SPL reaction specification structures followed by some examples of documents with reaction data: predicted single-step reactions, a two-step synthesis, an enzymatic reaction, an example how to represent a reaction center, a patent, and a fully annotated reaction with by-products. Special attention is given to a mechanism for atom-atom mapping of reactions as well as to the possibility to integrate Reaction SPL with laboratory automation equipment, in particular automated synthesis devices.

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“…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.…”

Section: Location Of Modifications In Amino Acid Residuesmentioning

confidence: 99%

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

Minkiewicz

¹

,

Darewicz

²

,

Iwaniak

³

et al. 2021

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Phosphorylation represents one of the most important modifications of amino acids, peptides, and proteins. By modifying the latter, it is useful in improving the functional properties of foods. Although all these substances are broadly annotated in internet databases, there is no unified code for their annotation. The present publication aims to describe a simple code for the annotation of phosphopeptide sequences. The proposed code describes the location of phosphate residues in amino acid side chains (including new rules of atom numbering in amino acids) and the diversity of phosphate residues (e.g., di- and triphosphate residues and phosphate amidation). This article also includes translating the proposed biological code into SMILES, being the most commonly used chemical code. Finally, it discusses possible errors associated with applying the proposed code and in the resulting SMILES representations of phosphopeptides. The proposed code can be extended to describe other modifications in the future.

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ReactionCode: format for reaction searching, analysis, classification, transform, and encoding/decoding

Cited by 11 publications

References 29 publications

Reaction SPL - extension of a public document markup standard to chemical reactions

Reaction SPL - extension of a public document markup standard to chemical reactions

Reaction SPL – extension of a public document markup standard to chemical reactions

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

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