LIGAND: chemical database for enzyme reactions

Area of Science:

• Bioinformatics
• Molecular Biology
• Computational Chemistry

Background:

• Existing molecular biology databases primarily focus on sequence and structural data of macromolecules.
• There is a need to computerize molecular interactions and include non-macromolecular components like metabolic compounds and metal ions for a comprehensive understanding of cellular functions.
• Public databases lack organized information on these essential building blocks of life.

Purpose of the Study:

• To develop the LIGAND chemical database to address limitations in existing molecular biology databases.
• To computerize information on enzymatic reactions, including enzymes, compounds, and their interactions.
• To provide a foundation for the reconstruction and computation of metabolic pathways.

Main Methods:

• Developed a two-section database: ENZYME and COMPOUND.
• ENZYME section extends previous work, containing 3303 enzymes and 2976 enzymatic reactions in a machine-readable format.
• COMPOUND section newly constructed with nomenclature and chemical structures for 5383 compounds, featuring cross-references generated by DBGET/LinkDB.

Main Results:

• The LIGAND database integrates information on 3303 enzymes and 5383 chemical compounds.
• Rich cross-reference information links chemical and biological databases, facilitating data integration.
• The database is updated daily and tightly coupled with the KEGG metabolic pathway database.

Conclusions:

• LIGAND provides a crucial resource for understanding molecular interactions and cellular functions.
• The database enhances the linkage between chemical and biological information systems.
• LIGAND serves as a foundational tool for metabolic pathway analysis and computational biology.