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---
license: mit
tags:
- binding-affinity
- biology
- chemistry
pretty_name: Binding Affinity
configs:
- config_name: default
data_files:
- split: train
path: "train.parquet"
- split: "combined"
path:
- "train.parquet"
- "test.parquet"
- "val.parquet"
- split: davis
path: "davis.parquet"
- split: davis_filtered
path: "davis-filtered.parquet"
- split: kiba
path: "kiba.parquet"
- split: pdbbind_2020_general
path: "pdbbind-2020-general.parquet"
- split: pdbbind_2020_refined
path: "pdbbind-2020-refined.parquet"
- split: pdbbind_2013_core
path: "pdbbind-2013-core.parquet"
- split: bindingdb_ic50
path: "bindingdb-ic50.parquet"
- split: bindingdb_ki
path: "bindingdb-ki.parquet"
- split: bindingdb_kd_filtered
path: "bindingdb-kd-filtered.parquet"
- split: bindingdb_kd
path: "bindingdb-kd.parquet"
- split: glaser
path: "glaser.parquet"
- split: drug_screen_test
path: "test_1000_drugs.parquet"
- split: test_25_targets_40_percent_similarity
path: "test_25_targets_40_percent_similarity.parquet"
- split: test_25_targets_60_percent_similarity
path: "test_25_targets_60_percent_similarity.parquet"
- split: test_25_targets_80_percent_similarity
path: "test_25_targets_80_percent_similarity.parquet"
---
# Binding Affinity Dataset
## Overview
This dataset is a comprehensive collection of protein-ligand binding affinity data, compiled from multiple sources. The dataset is structured with multiple splits, each corresponding to a specific source:
- train split
- test split
- validation split
- combined split
- davis split
- davis filtered split
- kiba split
- pdbbind 2020 combined split
- pdbbind 2020 refined split
- bindingdb ic50 split
- bindingdb kd split
- bindingdb kd filtered split
- bindingdb ki split
- glaser split
In addition to these source-specific splits, a main training split is provided that combines and aggregates data from all these sources.
## Training Dataset Composition
The training split is a comprehensive aggregation of multiple molecular binding datasets:
- Davis-filtered dataset
- PDBBind 2020 Combined dataset
- BindingDB IC50 dataset
- BindingDB Ki dataset
- BindingDB Kd Filtered dataset
- Glaser dataset
## Preprocessing Steps
1. **Dataset Merging**: All specified datasets were combined into a single dataset.
2. **Duplicate Removal**: Duplicate entries were dropped to ensure data uniqueness.
3. **Binding Affinity Normalization**:
- Entries with a binding affinity of 5 were reduced
- For duplicate protein-ligand pairs, the mean binding affinity was calculated
## Data Sources
| Dataset | Source | Notes |
|---------|--------|-------|
| bindingdb_ic50.parquet | [TDC Python Package](https://tdcommons.ai/) | Therapeutic Data Commons |
| bindingdb_kd.parquet | [TDC Python Package](https://tdcommons.ai/) | Therapeutic Data Commons |
| bindingdb_kd_filtered.parquet | Manually Filtered | See `standardize_data.ipynb` |
| bindingdb_ki.parquet | [TDC Python Package](https://tdcommons.ai/) | Therapeutic Data Commons |
| davis.parquet | [TDC Python Package](https://tdcommons.ai/) | Therapeutic Data Commons |
| davis_filtered.parquet | [Kaggle Dataset](https://www.kaggle.com/datasets/christang0002/davis-and-kiba) | Filtered Davis dataset |
| kiba.parquet | [TDC Python Package](https://tdcommons.ai/) | Therapeutic Data Commons |
| pdbbind_2020_combined.parquet | [PDBBind](https://www.pdbbind.org.cn/) | Combined PDBBind 2020 dataset |
| pdbbind_2020_refined.parquet | [PDBBind](https://www.pdbbind.org.cn/) | Refined PDBBind 2020 dataset |
| glaser.parquet | [HuggingFace Dataset](https://huggingface.co/datasets/jglaser/binding_affinity) | Glaser binding affinity dataset |
## Dataset Columns
| Column | Description |
|--------|-------------|
| `seq` | Protein sequence |
| `smiles_can` | Canonical SMILES representation of the ligand |
| `affinity_uM` | Binding affinity in micromolar (µM) concentration |
| `neg_log10_affinityM` | Negative logarithm (base 10) of the affinity in molar concentration |
| `affinity_norm` | Normalized binding affinity |
| `affinity_mean` | Mean binding affinity for duplicate protein-ligand pairs |
| `affinity_std` | Standard deviation of binding affinity for duplicate protein-ligand pairs |œ |