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metadata

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	Therapeutic Data Commons
bindingdb_kd.parquet	TDC Python Package	Therapeutic Data Commons
bindingdb_kd_filtered.parquet	Manually Filtered	See `standardize_data.ipynb`
bindingdb_ki.parquet	TDC Python Package	Therapeutic Data Commons
davis.parquet	TDC Python Package	Therapeutic Data Commons
davis_filtered.parquet	Kaggle Dataset	Filtered Davis dataset
kiba.parquet	TDC Python Package	Therapeutic Data Commons
pdbbind_2020_general.parquet	PDBBind	General PDBBind 2020 dataset
pdbbind_2020_refined.parquet	PDBBind	Refined PDBBind 2020 dataset
pdbbind_2013_core.parquet	PDBBind	Core PDBBind 2013 dataset
glaser.parquet	HuggingFace Dataset	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