NAR Molecular Biology Database Collection entry number 979
Liu T., Lin Y., Wen X., Jorissen R.N. and Gilson M.K.
Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA

Database Description

BindingDB ( curates measured binding affinities for the association ofproteins with small organic molecules. Data are drawn from thescientific literature, focusing on proteins that are known orpotential drug targets, and for which structural data is available inthe Protein Data Bank. The curated data include detailed experimentalconditions, such as pH, temperature, and solution composition.Examples of target proteins for which substantial data sets have beencollected include anthrax lethal factor, HIV protease, HIV reversetranscriptase, and various kinases and caspases. The database allowsquerying by target and compound name, target protein sequence,chemical substructure and similarity, and PubMed ID and PDB codes.

Recent Developments

BindingDB now provides well over 20,000 measurements involving morethan 10,000 different small organic molecules. Data sets resultingfrom queries can be downloaded as SDfiles, and the web-site alsoprovides virtual screening tools that allow the user to upload acompound database as an SDfile and search for compounds likely to beactive, based upon a set of known actives for a given target.


The authors gratefully acknowledge prior support bythe National Institute of Standards and Technology and the NationalScience Foundation (Grant Number 9808318), and current support by theNational Institute of General Medical Sciences, NIH (Grant NumberGM070064). The contents of this paper are solely the responsibility ofthe authors and do not necessarily represent the official views of thesponsors.


1.Chen, X., Liu, M., Gilson, M.K. (2002) BindingDB: A Web-accessible molecular recognition database. Combinatorial Chemistry and High Throughput Screening 4:719-725.
2. Chen, X., Lin, Y., Liu, M., Gilson, M.K. (2002) The Binding Database: Data management and interface design. Bioinformatics 18:130-139.
3. Chen, X., Liu, M., Gilson, M.K. (2002) The Binding Database: Overview and user's guide. Biopolymers/Nucleic Acid Science 61:127-141.

Subcategory: Protein properties

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