These files updated when new data are added, usually weekly
- Many users find the tab-separated value (TSV) files easiest to work with. These have one row for each binding measurement, so each row has the SMILES string of a ligand, and these files can easily be loaded into spreadsheet programs like Excel and LibreOffice Calc. Detailed documentation of our TSV format is available here.
- If you have special requirements or suggestions, please contact us. We will do our best to help.
- Full BindingDB Database Dump
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- Purchasable Compounds by Target
For each Target, this file (purchase_target_10000.tsv: 5.80 MB, updated 2024-04-25) lists all purchasable compounds we know of having affinity better than 10 uM, along with catalog links and pricing. Targets with no compounds like this are omitted. Contact us if you would like similar files with different cutoff criteria.
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- Ligand-Target-Affinity Datasets*
- All data in BindingdDB
- Only data curated from articles by BindingDB
- Only data in BindingDB drawn from ChEMBL
- Only data in BindingDB drawn from Patents
- Only data in BindingDB drawn from PubChem
- Only data in BindingDB drawn from PDSP Ki
- Only CSAR data in BindingDB
- Only data in BindingDB directly provided by Prof. Palmer Taylor, UCSD
- Only isothermal titration calorimetry (ITC) data in BindingDB
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- Lists and identifier mappings
- Validation sets
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- KNIME Workflows
The BindingDB team has developed KNIME workflows for easy retrieval of BindingDB data, and for predictions of protein targets. KNIME is a graphical workbench for processing and retrieving data. The open integration platform provides over 1000 modules (nodes), including those of the KNIME community and its extensive partner network. The main advantage of retrieving data this way is flexibility; you can process the data further by adding your own nodes, and you can save the data to local disk in the format of choice. To use, simply import this workflow into the KNIME desktop, available here. In either workflow path, open the first node by double-clicking, and enter your query. Then click .Run.; the output will be collected in the final node. The workflow can be downloaded from here:BindingDB_workflows.knwf ( 534.84 KB, updated 2018-03-23)
In order for the workflows to run properly, the following KNIME extensions need to be installed:
- KNIME & Extensions
- KNIME Community Contributions - Cheminformatics
- KNIME Labs Extensions
- Marvin Chemistry Extensions
*_2D.sdf: compound structures provided with 2-dimensional coordinates
*_3D.sdf: compound structures provided with 3-dimensional coordinates computed with
Vconf (-m prep)
* _terse_: Each Compound appears once, with multiple Target data for it in the data blocks
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