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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
Summary
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.
- 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.
