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. As of March, 2011, BindingDB contains about 650,000 binding data, for 5,700 protein targets and 280,000 small molecules. BindingDB also includes a small collection of host–guest binding data of interest to chemists studying supramolecular systems. The purpose of BindingDB is to support medicinal chemistry and drug discovery via literature awareness and development of structure-activity relations (SAR and QSAR); validation of

computational chemistry Computational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of m ...

and

molecular modelling Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials sci ...

approaches such as docking, scoring and free energy methods; chemical biology and chemical genomics; and basic studies of the physical chemistry of

molecular recognition The term molecular recognition refers to the specific interaction between two or more molecules through noncovalent bonding such as hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, π-π interactions, halogen b ...

. 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 scientific literature by the BindingDB project, selected

PubChem PubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information (NCBI), a component of the National Library of Medicine, which is part of ...

confirmatory BioAssays, and

ChEMBL ChEMBL or ChEMBLdb is a manually curated chemical database of bioactive molecules with drug-like properties. It is maintained by the European Bioinformatics Institute (EBI), of the European Molecular Biology Laboratory ( EMBL), based at the Wel ...

entries for which a well-defined protein target ("TARGET_TYPE='PROTEIN'") is provided.

History and Funding

The BindingDB project was conceived in the mid-1990s, based upon recognition of the broad value of quantitative affinity data and the inadequacy of journal articles as a means of making these data accessible. A

NIST The National Institute of Standards and Technology (NIST) is an agency of the United States Department of Commerce whose mission is to promote American innovation and industrial competitiveness. NIST's activities are organized into physical sci ...

-sponsored workshop in September 1997 validated the concept, and funding from the

NSF NSF may stand for: Political organizations *National Socialist Front, a Swedish National Socialist party *NS-Frauenschaft, the women's wing of the former German Nazi party *National Students Federation, a leftist Pakistani students' political gr ...

and NIST enabled initial development of the database with a collection of data for systems of many types, including protein-ligand, protein-protein, and host–guest binding. However, hopes that the database would be populated primarily through depositions by experimentalists were not borne out, and it became clear that the project would have to take responsibility for extracting data from the literature. Given the vastness of the molecular recognition literature and limitations in available resources, this meant that creating a useful database would require limiting attention to a well-defined set of high-value binding data. The decision was taken to focus on binding data for small molecules with proteins that are drug-targets, or potential drug-targets, and for which the three-dimensional structure is available in the PDB or can potentially be modeled to high accuracy based upon the structure of a similar protein. This choice would aid drug-discovery for the selected targets, as well as the development of both ligand-based and structure-based methods of computational ligand-design. This is the current focus of BindingDB, which is led b
Michael Gilson
based at

UC San Diego The University of California, San Diego (UC San Diego or colloquially, UCSD) is a public university, public Land-grant university, land-grant research university in San Diego, California. Established in 1960 near the pre-existing Scripps Insti ...

Skaggs School of Pharmacy and Pharmaceutical Sciences The Skaggs School of Pharmacy and Pharmaceutical Sciences is a graduate-level pharmacy school at the University of California, San Diego. It offers five educational programs: * Doctor of Pharmacy (Pharm.D.) degree awarded in a four-year progr ...

, and supported by a grant from the

NIH The National Institutes of Health, commonly referred to as NIH (with each letter pronounced individually), is the primary agency of the United States government responsible for biomedical and public health research. It was founded in the late ...

Capabilities

BindingDB's web-interface provides a range of browsing, query and data download tools. These include browsing by the name of a protein Target or by journal citation, query by chemical similarity and substructure, and downloads by target or query result.

References

External links

BindingDB.org

BindingDB tutorial information and documentation

Video tutorials for basic BindingDB tasks
{dead link, date=November 2016 , bot=InternetArchiveBot , fix-attempted=yes Medicinal chemistry Biological databases

History and Funding

Capabilities

See also

References

External links