Datasets › BindingDB
BindingDB (The Binding Database)
BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. As of May 27, 2022, BindingDB contains 41,296 Entries, each with a DOI, containing 2,519,702 binding data for 8,810 protein targets and 1,080,101 small molecules. There are 5,988 protein-ligand crystal structures with BindingDB affinity measurements for proteins with 100% sequence identity, and 11,442 crystal structures allowing proteins to 85% sequence identity.You can also use BindingDB data through the Registry of Open Data on AWS: https://registry.opendata.aws/binding-db. This dataset using the split by TransformerCPI(doi.org/10.1093/bioinformatics/btaa524)
Benchmarks archive 2025-07-28
All 2 leaderboards whose dataset resolves to this page shown (sort by any header). "First row" is the archive's own first row at snapshot, in the archive's row order; nothing here re-ranks and metric direction is not asserted.
| First row (archive order) | Paper | Code | ||||
|---|---|---|---|---|---|---|
| Drug Discovery | BindingDB | AttentionSiteDTI AUC 0.9717 | AttentionSiteDTI: an interpretable graph-based model for... | yazdanimehdi/AttentionSiteDTI | 4 | Compare |
| Drug Discovery | BindingDB IC50 | DeepDTA Pearson Correlation 0.848 | DeepDTA: Deep Drug-Target Binding Affinity Prediction | kexinhuang12345/DeepPurpose +3 | 2 | Compare |
Papers archive 2025-07-28
6 shown of 6 papers with a leaderboard row on this dataset's benchmarks, newest first. The archive's own "papers using this dataset" list was never published, so this is the benchmark-backed subset; the archive's count for this dataset is 10. The Syntology column is from Syntology's graph (read 2026-09-24), stated per sample; it is not part of any archive number.
| Date | Samples run Syntology | |||
|---|---|---|---|---|
| AttentionSiteDTI: an interpretable graph-based model for drug-target interaction prediction using NLP sentence-level relation classification | 1 | 1 | 12 Jul 2022 | not harvested |
| An adaptive graph learning method for automated molecular interactions and properties predictions | 1 | 1 | 23 Jun 2022 | not harvested |
| Drug–target affinity prediction using graph neural network and contact maps | 1 | 1 | 1 Jun 2020 | not harvested |
| TransformerCPI: improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments | 2 | 1 | 19 May 2020 | not harvested |
| DeepAffinity: Interpretable Deep Learning of Compound-Protein Affinity through Unified Recurrent and Convolutional Neural Networks | 2 | 1 | 20 Jun 2018 | ran 2 of 2 samples (0 unverified; 2 pointer-only for licence) |
| DeepDTA: Deep Drug-Target Binding Affinity Prediction | 4 | 1 | 30 Jan 2018 | not harvested |
Dataset loaders archive 2025-07-28
No loader listed in the archive.
Tasks archive 2025-07-28
License archive 2025-07-28
No licence recorded in the archive. Absence here is not a statement about the dataset's terms.
Modalities archive 2025-07-28
No modality tagged.
Languages archive 2025-07-28
No language tagged.
Variants archive 2025-07-28
- BindingDB
- BindingDB IC50
2 variant names, as the archive lists them.
Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections