PDB Bind

PDB Bind is a comprehensive database that provides experimentally measured binding affinity data (Kd, Ki, IC50) for biomolecular complexes in the Protein Data Bank (PDB). It serves as a critical resource for computational chemists and structural biologists by linking 3D structural information with quantitative binding data. The database is widely used for developing and validating scoring functions in molecular docking, virtual screening, and structure-based drug design.

Also known as: PDBBind, PDB-Bind, Protein Data Bank Binding Database, Binding Affinity Database, PDB Binding Data

Why learn PDB Bind?

Developers should learn about PDB Bind when working in computational biology, bioinformatics, or drug discovery, as it provides essential ground-truth data for training machine learning models and evaluating docking algorithms. It is particularly valuable for building predictive models of protein-ligand interactions, benchmarking computational tools, and understanding structure-activity relationships in pharmaceutical research.

Learning Resources

• docs: PDB Bind Official Website
• docs: PDB Bind Database Overview Paper
• tutorial: Tutorial on Using PDB Bind for Docking Validation
• video: Video Introduction to Binding Affinity Databases
• book: Book: 'Computational Drug Discovery and Design' (Chapter on PDB Bind)