BindingDB is a publicly accessible database containing approximately 20,000 experimentally determined protein–ligand binding affinities for 110 protein targets and 11,000 small molecule ligands. The data are sourced from the scientific literature, focusing on proteins that are drug targets or candidates with structural data in the Protein Data Bank (PDB). The database supports various query types, including chemical structure, substructure, similarity, protein sequence, and affinity ranges. Data can be downloaded as annotated SD files for further analysis or used for virtual screening of user-uploaded compound databases. BindingDB links data to PDB structures via PDB IDs and to PubMed via PubMed IDs. BindingDB was created to address the need for a centralized database of binding affinities, which are often published in scientific journals but are difficult to access and analyze. The database provides tools for querying, analyzing, and downloading binding data, as well as virtual screening capabilities. It includes data from enzyme inhibition studies and isothermal titration calorimetry. The database also allows users to build and download datasets for further analysis. BindingDB complements other databases by focusing on proteins with known structures, allowing it to avoid overlap with databases that collect data for membrane proteins with unavailable structures. The database includes data for various targets, including anthrax lethal factor, caspases, kinases, HIV protease, and reverse transcriptase. It differs from other databases like KiBank, which includes data for proteins without structural information. The database provides a web interface for querying, downloading, and virtual screening. Users can upload their own ligand data and use machine-learning methods to rank compounds based on similarity, binary kernel discrimination, or support vector machines. The database is freely accessible and requires registration for downloading SD files. Users are encouraged to provide feedback on data sets and website features. Works using BindingDB should cite the original paper. Funding for the database was provided by the National Institute of Standards and Technology and the National Science Foundation.BindingDB is a publicly accessible database containing approximately 20,000 experimentally determined protein–ligand binding affinities for 110 protein targets and 11,000 small molecule ligands. The data are sourced from the scientific literature, focusing on proteins that are drug targets or candidates with structural data in the Protein Data Bank (PDB). The database supports various query types, including chemical structure, substructure, similarity, protein sequence, and affinity ranges. Data can be downloaded as annotated SD files for further analysis or used for virtual screening of user-uploaded compound databases. BindingDB links data to PDB structures via PDB IDs and to PubMed via PubMed IDs. BindingDB was created to address the need for a centralized database of binding affinities, which are often published in scientific journals but are difficult to access and analyze. The database provides tools for querying, analyzing, and downloading binding data, as well as virtual screening capabilities. It includes data from enzyme inhibition studies and isothermal titration calorimetry. The database also allows users to build and download datasets for further analysis. BindingDB complements other databases by focusing on proteins with known structures, allowing it to avoid overlap with databases that collect data for membrane proteins with unavailable structures. The database includes data for various targets, including anthrax lethal factor, caspases, kinases, HIV protease, and reverse transcriptase. It differs from other databases like KiBank, which includes data for proteins without structural information. The database provides a web interface for querying, downloading, and virtual screening. Users can upload their own ligand data and use machine-learning methods to rank compounds based on similarity, binary kernel discrimination, or support vector machines. The database is freely accessible and requires registration for downloading SD files. Users are encouraged to provide feedback on data sets and website features. Works using BindingDB should cite the original paper. Funding for the database was provided by the National Institute of Standards and Technology and the National Science Foundation.