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

Abstract

BindingDB () 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.

The Protein Data Bank archive as an open data resource

“…More than 400 million coordinate sets were downloaded in 2013 from the wwPDB partner sites. Both the utility and the uniformity of PDB data have enabled the development of other databases and datarelated resources, including resources for drug discovery (for a review see [32]); resources focused on small molecules and ligands such as ChEMBL [33], DrugBank [34], BindingDB [35], BindingMOAD [36], and PDBBind [37]; protein structure classification and annotation resources, such as CATH [38,39], SCOP [40][41][42], and PDBsum [43,44]; and focused, specialty annotation resources such as Protein Data Bank of Transmembrane Proteins (PDBTM) [45], ArchDB for functional loops in structures [46], and 3did for protein-protein interaction surfaces [47]. These resources are frequently compiled in the annual Database Issue of Nucleic Acids Research.…”

An enriched structural kinase database to enable kinome‐wide structure‐based analyses and drug discovery

“…Other databases have integrated known binding affinities of ligands with the relevant complex structures. [12][13][14] We have recently developed both a general, ligand-focused protein relational database (PRDB) and protein family focused knowledge bases, which in essence are subsets of PRDB. Currently knowledge bases have been developed for the matrix metalloproteins (MMP's) and kinases (Mobilio et al, Submitted).…”

ChemTreeMap: an interactive map of biochemical similarity in molecular datasets

“…For huge datasets, such as ChEMBL (Gaulton et al, 2012), BindingDB (Liu et al, 2007) and ChemBank (Seiler et al, 2008), the molecules need to be clustered by similarity to reduce the size of the task. An interactive display of millions of leafs is not possible with current technology.…”

“…To demonstrate ChemTreeMap, we have chosen diverse biomolecular datasets ranging from thousands to millions of molecules. To show chem-data overlap, we use some of the largest datasets with bioactivity data: ChEMBL v. 20 (Gaulton et al, 2012), BindingDB (Liu et al, 2007) and ChemBank (Seiler et al, 2008).…”