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Updated: May 31, 2026

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods
05:34

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods

Published on: June 6, 2025

CBR-db: A Cheminformatic Database for Biochemical Reaction Analysis.

Louie Slocombe1, Camerian Millsaps2, M Reza Shahjahan2

  • 1Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, Arizona 85287-0506, United States.

ACS Synthetic Biology
|May 28, 2026
PubMed
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We introduce CBR-db, a novel database offering chemical property data for biochemical reactions and molecules. This resource provides chemically consistent analyses crucial for understanding metabolism and designing biochemical systems.

Area of Science:

  • Biochemistry
  • Cheminformatics
  • Bioinformatics

Background:

  • Biochemical reactions and small molecules are fundamental to life.
  • Existing databases often lack comprehensive, chemically consistent property data.
  • Understanding molecular properties is key to metabolism and synthetic biology.

Purpose of the Study:

  • To present CBR-db, a new database of chemical properties for biochemical compounds and reactions.
  • To provide the first chemically consistent analyses for a large set of biological molecules and reactions.
  • To highlight the utility of cheminformatic data for biological research.

Main Methods:

  • Compiled data from the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the ATLAS of Biochemistry.
  • Performed chemically consistent analyses including atom tracking and property calculations.
Keywords:
assembly indexatom trackingbiochemical datachemical spacecheminformaticsreaction similarity

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  • Included data on compound properties, reaction similarity, chiral centers, and thermodynamics.

    • Main Results:

    • CBR-db contains data for 148,673 reactions and 18,716 small molecules.
    • Detailed chemical property data, atom tracking, and thermodynamic properties are provided.
    • The database is designed for continuous updates, open-source access, and reproducibility.

    Conclusions:

    • CBR-db offers a valuable resource at the intersection of cheminformatics and bioinformatics.
    • The data supports research in metabolism, synthetic biochemical design, and evolutionary biochemistry.
    • This database facilitates a deeper understanding of molecular properties and reaction mechanisms.