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

Abstract

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.

Evidence-Based Precision Oncology with the Cancer Targetome

“…However, IUPHAR typically provides only one experimental binding assay value for each drug-target interaction, so we also included an aggregated bioactivity database (BindingDB) in our collection efforts for the Cancer Targetome. BindingDB provides a wide coverage of binding assay data by aggregating across the scientific literature as well as from other bioactivity resources such as ChEMBL and PubChem [45]. Across four resources (DrugBank, Therapeutic Targets Database, IUPHAR, and BindingDB), we retrieved a total of 137 drugs and 658 targets participating in a total of 6385 unique drug-target relationships.…”

Computer-aided drug design: time to play with novel chemical matter

“…The emergence of cryo-electron microscopy ensures that structural information will continue to grow at a fast rate in the years to come [15]. On the ligand side, several initiatives are making it ever easier to access and use wellcurated bioactivity data [16,17].…”

Current situation and future usage of anticancer drug databases

“…pharmgkb.org). (4) Binding Database (BindingDB) [41] is the first online resource of experimentally validated protein-ligand interaction data with over a million entries. It provides easy access to focused datasets such as the affinity information with a specific protein target, and extensive analyses utilizing a vast and comprehensive data set.…”