---
license: mit
tags:
- binding-affinity
- biology
- chemistry
pretty_name: Binding Affinity
configs:
- config_name: default
  data_files:
  - split: train
    path: "glaser.parquet"
  - split: val
    path: "pdbbind-2013-core.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_general_equal_only
    path: "pdbbind-2020-general-equal-only.parquet"
  - split: pdbbind_2020_general_ic50
    path: "pdbbind-2020-general-ic50.parquet"
  - split: pdbbind_2020_general_ic50_equal_only
    path: "pdbbind-2020-general-ic50-equal-only.parquet"
  - split: pdbbind_2020_general_ki
    path: "pdbbind-2020-general-ki.parquet"
  - split: pdbbind_2020_general_ki_equal_only
    path: "pdbbind-2020-general-ki-equal-only.parquet"
  - split: pdbbind_2020_general_kd
    path: "pdbbind-2020-general-kd.parquet"
  - split: pdbbind_2020_general_kd_equal_only
    path: "pdbbind-2020-general-kd-equal-only.parquet"
  - split: pdbbind_2020_refined
    path: "pdbbind-2020-refined.parquet"
  - split: pdbbind_2020_refined_ki
    path: "pdbbind-2020-refined-ki.parquet"
  - split: pdbbind_2020_refined_kd
    path: "pdbbind-2020-refined-kd.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"
---

# 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 (glaser.parquet)
- val split (pdbbind-2013-core.parquet)
- davis split
- davis_filtered split
- kiba split
- pdbbind_2020_general split
- pdbbind_2020_refined split
- pdbbind_2013_core split
- bindingdb_ic50 split
- bindingdb_ki split
- bindingdb_kd_filtered split
- bindingdb_kd split
- glaser split

## Training Dataset Composition

The training split uses the Glaser dataset, while the validation split uses the PDBBind 2013 Core dataset.

## 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_general.parquet | [PDBBind](https://www.pdbbind.org.cn/) | General PDBBind 2020 dataset |
| pdbbind_2020_refined.parquet | [PDBBind](https://www.pdbbind.org.cn/) | Refined PDBBind 2020 dataset |
| pdbbind_2013_core.parquet | [PDBBind](https://www.pdbbind.org.cn/) | Core PDBBind 2013 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 |