Databases of ligand-binding pockets and protein-ligand interactions

Area of Science:

• Biochemistry
• Structural Biology
• Bioinformatics

Background:

• Numerous databases exist for protein-ligand binding data, but the landscape is dynamic with frequent emergence and discontinuation of resources.
• These databases curate experimental and predicted data crucial for understanding molecular interactions.

Purpose of the Study:

• To review the current state of databases containing protein binding pockets and protein-ligand binding interactions.
• To provide an organized overview of available resources for researchers.

Main Methods:

• Compiled a list of currently available protein-ligand binding databases, identifying 53 active resources.
• Analyzed and categorized databases based on their goals, contents, and typical use cases.
• Examined variations in binding pocket definitions and pocket-finding methodologies across different databases.

Main Results:

• Identified 53 currently available databases for protein-ligand binding information.
• Demonstrated significant variation in how binding pockets are defined and characterized across different databases for the same protein.
• Organized databases into subgroups, detailing their specific aims and applications.

Conclusions:

• The current landscape of protein-ligand binding databases is diverse but faces challenges in consistency, sustainability, and accessibility.
• Researchers must be aware of the variations in pocket definitions and database content when utilizing these resources.
• Further efforts are needed to ensure the long-term viability and standardization of valuable scientific data repositories.