BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology

By Michael K. Gilson, Tiqing Liu, Michael Baitaluk, George Nicola, Linda Hwang, Jenny Chong. Nucleic Acids Res., 2015

1,423 citations recorded by the source corpus.

BindingDB, www.bindingdb.org, is a publicly accessible database of experimental protein-small molecule interaction data. Its collection of over a million data entries derives primarily from scientific articles and, increasingly, US patents. BindingDB provides many ways to browse and search for data of interest, including an advanced search tool, which can cross searches of multiple query types, including text, chemical structure, protein sequence and numerical affinities. The PDB and PubMed provide links to data in BindingDB, and vice versa; and BindingDB provides links to pathway information, the ZINC catalog of available compounds, and other resources. The BindingDB website offers specialized tools that take advantage of its large data collection, including ones to generate hypotheses for the protein targets bound by a bioactive compound, and for the compounds bound by a new protein of known sequence; and virtual compound screening by maximal chemical similarity, binary kernel discrimination, and support vector machine methods. Specialized data sets are also available, such as binding data for hundreds of congeneric series of ligands, drawn from BindingDB and organized for use in validating drug design methods. BindingDB offers several forms of programmatic access, and comes with extensive background material and documentation. Here, we provide the first update of BindingDB since 2007, focusing on new and unique features and highlighting directions of importance to the field as a whole.

Subfields: Computational Theory and Mathematics, Molecular Biology, Pharmacology

View Paper: https://www.semanticscholar.org/paper/d4921d6c5dfd0741026028745b63b450e4e81cd1

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Citations in the corpus

Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2 (2017, methodology): “From the database BindingDB [38], we retrieved 229 ligands that bind to the FXR protein with reported experimental IC50 data.”
PubChem 2019 update: improved access to chemical data (2018, neutral): “com/), SCRIPDB (25), and BindingDB (26).”
Interpretable Drug Target Prediction Using Deep Neural Representation (2018, background): “BindingDB [ Gilson et al. , 2016 ] is a public, web-accessible database of measured binding afﬁnities, focusing chieﬂy on the interactions of small molecules (drugs/drug candidates) and proteins (targets/target candidates).”
Systematic integration of biomedical knowledge prioritizes drugs for repurposing (2017, methodology): “…Pico and Himmelstein, 2015 ; Himmelstein and Pico, 2016a ) BindingDB CbG mixed CC BY 3.0 and CC BY-SA 3.0 2 OD RRID:SCR_000390 ( Chen et al., 2001 ; Gilson et al., 2016 ; Himmelstein and Gilson, 2015i ; Himmelstein et al., 2015d ) DisGeNET DaG ODbL 2 OD RRID:SCR_006178 ( Himmelstein, 2015f ;…”
PubChem BioAssay: 2017 update (2016, methodology): “The database also contains literature-based data including both publication driven depositions submitted by journal authors and those contributed by PDBbind (10), IUPHAR (11), Bind-ingDB (12), ChEMBL (13) and other literature curation projects.”
The ChEMBL database in 2017 (2016, methodology): “ChEMBL data is incorporated into a wide range of other resources including PubChem BioAssay (52), BindingDB (11), CanSAR (53), Open PHACTS (54), Open Targets (55) and the Target Central Resource Database/PHAROS (http: //juniper.”