BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of proteins considered to be candidate drug-targets with ligands that are small, drug-like molecules. BindingDB supports medicinal chemistry and drug discovery via literature awareness and development of structure-activity relations (SAR and QSAR); validation of computational chemistry and molecular modeling approaches such as docking, scoring and free energy methods; chemical biology and chemical genomics; and basic studies of the physical chemistry of molecular recognition. BindingDB also includes a small collection of host-guest binding data of interest to chemists studying supramolecular systems.
The data collection derives from a variety of measurement techniques, including enzyme inhibition and kinetics, isothermal titration calorimetry, NMR, and radioligand and competition assays. BindingDB includes data extracted from the literature and patents by the BindingDB project, selected PubChem confirmatory BioAssays, and ChEMBL entries for which a well defined protein target ("TARGET_TYPE='PROTEIN'") is provided. Data extracted by BindingDB typically includes more details regarding experimental conditions, etc. BindingDB currently contains about 2,791,311 binding data for 9,180 proteins and over 1,194,492 drug-like molecules. Data imported from ChEMBL are provided under their Creative Commons Attribution-Share Alike 3.0 Unported License. All data curated by BindingDB staff are provided under the Creative Commons Attribution 3.0 License.
- Background on Proteins, Small Molecules, and Binding
- How to Use BindingDB
- Search Templates in BindingDB
- Documentation of BindingDB's SDfile and TSV formats
- A caveat regarding protein Target sequences
- Important information about a BindingDB SDfile
- BindingDB Page on Wikipedia
BindingDB Affinity Statistics
- Gilson,M.K., Liu,T., Baitaluk,M., Nicola,G., Hwang, L. and Chong,J. BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology Nucleic Acids Research 44:D1045-D1053 (2015).[pdf]
- Liu,T., Lin,Y., Wen,X., Jorrisen, R.N. and Gilson,M.K. BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities Nucleic Acids Research 35:D198-D201 (2007).[pdf]
- Chen,X., Lin,Y. and Gilson,M.K. The Binding Database: Overview and User's Guide Biopolymers Nucleic Acid Sci. 61:127-141 (2002).[pdf]
- Chen,X., Lin,Y., Liu,M. and Gilson,M.K. The Binding Database: Data Management and Interface Design Bioinformatics 18:130-139(2002).[pdf]
- Chen,X., Liu,M., and Gilson,M.K. Binding DB: A web-accessible molecular recognition database J. Combi. Chem. High-Throughput Screen 4:719-725(2001).[pdf]