BindingDB
Encyclopedia
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 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
.
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
confirmatory BioAssays, and ChEMBL
entries for which a well-defined protein target ("TARGET_TYPE='PROTEIN'") is provided.
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 by Michael Gilson, based at UC San Diego’s Skaggs School of Pharmacy and Pharmaceutical Sciences, and supported by a grant from the NIH.
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
Host-guest chemistry
In supramolecular chemistry, host-guest chemistry describes complexes that are composed of two or more molecules or ions that are held together in unique structural relationships by forces other than those of full covalent bonds. Host-guest chemistry encompasses the idea of molecular recognition...
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 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
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, electrostatic and/or electromagnetic effects...
.
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
PubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information , a component of the National Library of Medicine, which is part of the United States National Institutes of Health . PubChem can...
confirmatory BioAssays, and ChEMBL
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 , based on the Wellcome Trust Genome Campus, Hinxton, UK. The database, originally known as StARlite, was developed by a...
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-sponsored workshop in September 1997 validated the concept, and funding from the NSFNSF
-Politics:* National Service Framework, any of a series of British government policies on medical care* National Socialist Front, a Swedish Nazi party* NS-Frauenschaft, the women's wing of the former German Nazi party...
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 by Michael Gilson, based at UC San Diego’s Skaggs School of Pharmacy and Pharmaceutical Sciences, and supported by a grant from the NIH.