|
--- |
|
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 |
