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About this collection

Extent

9 digital objects.

Cite This Work

Gilson, Michael K.; Liu, Tiqing (2023). BindingDB: Measured Binding Data for Protein-Ligand and Other Molecular Systems. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0HD7VVF

Description

This collection contains the data in BindingDB, a large database launched in 2000 that supports research, education and practice in drug discovery, pharmacology, computer-aided drug design, machine-learning and artificial intelligence, and related fields by collecting experimentally measured protein-small molecule binding data, as well as selected collections of other types of binding data, such as host-guest and protein-protein, chiefly from scientific articles and patents.

Date Collected

• 2000 to present

Date Issued

• 2023

Principal Investigator

• Gilson, Michael K.

Research Team Member

• Liu, Tiqing

Topics

• Affinity
• Antibody
• Artificial intelligence (AI)
• Binding
• Computational chemistry
• Database
• Dissociation constant (Kd)
• Domain: Biological sciences
• Domain: Biomedical and clinical sciences
• Domain: Chemical sciences
• Domain: Information and computing sciences
• Drug
• Drug discovery
• Free energy
• Half maximal inhibitory concentration (IC50)
• Host-guest
• Ligand
• Machine learning
• Medicinal chemistry
• Medicine
• Protein
• Protein-protein
• Simplified Molecular Input Line Entry System (SMILES)
• Small molecule
• UniProt

Formats

View formats within this collection

• data
• text

Language

• English

Identifier

Identifier: Michael K. Gilson: https://orcid.org/0000-0002-3375-1738

Identifier: Tiqing Liu: https://orcid.org/0000-0002-3429-9333

Doi: https://doi.org/10.6075/J0HD7VVF

Related Resources

Primary associated publication

• 2001: Chen, X., Liu, M., and Gilson, M.K. Binding DB: A web-accessible molecular recognition database J. Combi. Chem. High-Throughput Screen 4:719-725(2001). https://doi.org/10.2174/1386207013330670
• 2007: Liu, T., Lin, Y., Wen, X., Jorrisen, R.N. and Gilson, M.K. BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities Nucleic Acids Research 35:D198-D201 (2007). https://doi.org/10.1093/nar/gkl999
• 2016: Gilson, M.K., Liu, T., Baitaluk, M., Nicola, G., Hwang, L. and Chong, J. BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. Nucleic Acids Research 44:D1045-D1053 (2016). https://doi.org/10.1093/nar/gkv1072

Interactive viewer

• BindingDB website and database (bindingdb.org)

Reference

• ChEMBL (RRID:SCR_014042): https://www.ebi.ac.uk/chembl/
• Chemical Entities of Biological Interest (ChEBI) (RRID:SCR_002088): https://www.ebi.ac.uk/chebi/
• Drug Design Data Resource (D3R) (RRID:SCR_000497): https://drugdesigndata.org/
• DrugBank (RRID:SCR_002700): https://go.drugbank.com/
• International Union of Basic and Clinical Pharmacology / British Pharmacological Society (IUPHAR/BPS) Guide to Pharmacology (RRID:SCR_013077): https://www.guidetopharmacology.org/
• James B. Dunbar Jr., Richard D. Smith, Kelly L. Damm-Ganamet, Aqeel Ahmed, Emilio Xavier Esposito, James Delproposto, Krishnapriya Chinnaswamy, You-Na Kang, Ginger Kubish, Jason E. Gestwicki, Jeanne A. Stuckey, and Heather A. Carlson (2013). CSAR Data Set Release 2012: Ligands, Affinities, Complexes, and Docking Decoys. Journal of Chemical Information and Modeling 53 (8), 1842-1852. https://doi.org/10.1021/ci4000486
• KEGG: Kyoto Encyclopedia of Genes and Genomes: https://www.genome.jp/kegg/
• PDSP Ki: https://pdsp.unc.edu/databases/kidb.php
• PubChem (RRID:SCR_004284): https://pubchem.ncbi.nlm.nih.gov/
• PubMed (RRID:SCR_004846): https://pubmed.ncbi.nlm.nih.gov/
• UniProt Knowledgebase (UniProtKB) (RRID:SCR_002380): https://www.uniprot.org/
• Worldwide Protein Data Bank (wwPDB) (RRID:SCR_006555): https://www.wwpdb.org/
• ZINC (RRID:SCR_008596): https://zinc.docking.org/