BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities

TLDR

BindingDB is a publicly accessible database containing approximately 20,000 experimentally determined protein–ligand binding affinities for 110 protein targets and 11,000 small molecules. The database aggregates literature‑derived data on drug‑target proteins with available PDB structures, offers diverse query options (structure, sequence, affinity, etc.), and provides downloadable annotated datasets linked to PDB and PubMed identifiers.

Abstract

BindingDB (Author Webpage) is a publicly accessible database currently containing ∼20 000 experimentally determined binding affinities of protein–ligand complexes, for 110 protein targets including isoforms and mutational variants, and ∼11 000 small molecule ligands. The data are extracted from the scientific literature, data collection focusing on proteins that are drug-targets or candidate drug-targets and for which structural data are present in the Protein Data Bank. The BindingDB website supports a range of query types, including searches by chemical structure, substructure and similarity; protein sequence; ligand and protein names; affinity ranges and molecular weight. Data sets generated by BindingDB queries can be downloaded in the form of annotated SDfiles for further analysis, or used as the basis for virtual screening of a compound database uploaded by the user. The data in BindingDB are linked both to structural data in the PDB via PDB IDs and chemical and sequence searches, and to the literature in PubMed via PubMed IDs.