Gilson, Michael K.; Liu, Tiqing; Hwang, Linda (2024). BindingDB Dataset, January 1, 2024. In BindingDB: Measured Binding Data for Protein-Ligand and Other Molecular Systems. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0BP02ZT

This object is the BindingDB dataset as of January 1, 2024.

The core data for a given binding measurement comprises the identity of the two molecules involved, usually a protein and a small organic molecule; a measured indicator of their affinity, such as a dissociation constant or IC50; and the identity of the document from which the measurement was curated. Proteins are identified primarily by UniProt ID and small organic molecules by SMILES strings.

This BindingDB release contains about 2.6 million experimental binding data.

• Date of data collection: 2000 to 2023. Date of version: 2024-01-01.

• 2024

• Gilson, Michael K.

• Hwang, Linda
• Liu, Tiqing

Data curated by BindingDB were collected from articles and patents using a semi-automated procedure. We first work from the source document to automatically preload a representation of the data into a web-based curation interface. Human curators then examine the preloaded data, compare it with the source document, and make corrections as needed. The corrected curation is then inspected by a second curator and any proposed corrections are discussed and made if needed. Occasionally, a user will contact BindingDB with a proposed correction. Each such proposal is reviewed individually and made if warranted.

The Oracle data dump was exported from Oracle 12c Enterprise Edition release 12.2.0.1.0- 64-bit production. The MySQL dump was exported from MySQL version 8.0.26.

All data curated by BindingDB staff are provided under the Creative Commons Attribution 4.0 License. Data imported from ChEMBL are provided under their Creative Commons Attribution-Share Alike 3.0 Unported License.

BindingDB has been supported by the National Institute of General Medical Sciences (NIH grants R24GM14423 and R01GM070064), by NSF grant 9808318, and by the National Institute of Standards and Technology. Its contents are solely the responsibility of the authors and do not necessarily reflect the official views of the sponsors. ChemAxon and OpenEye also have supported BindingDB through their academic software licensing programs.

• Affinity
• Algorithm: Semi-supervised learning
• Algorithm: Supervised learning
• Algorithm: Unsupervised learning
• Antibody
• Artificial intelligence
• Binding
• Computational chemistry
• Database
• Dissociation constant (Kd)
• 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
• Task: Classification
• Task: Clustering
• Task: Dimensionality reduction
• Task: Feature extraction
• Task: Multiclass classification
• Task: Regression
• UniProt

• data
• text

• English

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

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

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: https://www.ebi.ac.uk/chembl/
• Chemical Entities of Biological Interest (ChEBI): https://www.ebi.ac.uk/chebi/
• Community Structure-Activity Resource (CSAR): http://www.csardock.org/
• Drug Design Data Resource (D3R): https://drugdesigndata.org/
• DrugBank: https://go.drugbank.com/
• International Union of Basic and Clinical Pharmacology / British Pharmacological Society Guide to Pharmacology: https://www.guidetopharmacology.org/
• KEGG: Kyoto Encyclopedia of Genes and Genomes: https://www.genome.jp/kegg/
• PDSP Ki: https://pdsp.unc.edu/databases/kidb.php
• Protein Data Bank archive (PDB): https://www.wwpdb.org/
• PubChem: https://pubchem.ncbi.nlm.nih.gov/
• PubMed: https://pubmed.ncbi.nlm.nih.gov/
• UniProt Knowledgebase (UniProtKB): https://www.uniprot.org/
• ZINC: https://zinc.docking.org/

Creative Commons Attribution 4.0 International Public License

• UC Regents

Under copyright (US)

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Constraint(s) on Use: This work is protected by the U.S. Copyright Law (Title 17, U.S.C.). Use of this work beyond that allowed by "fair use" or any license applied to this work requires written permission of the copyright holder(s). Responsibility for obtaining permissions and any use and distribution of this work rests exclusively with the user and not the UC San Diego Library. Inquiries can be made to the UC San Diego Library program having custody of the work.

Research Data Curation Program, UC San Diego, La Jolla, 92093-0175 (https://lib.ucsd.edu/rdcp)

2024-07-10