Datasets:

Leash-Biosciences
/

mf-pcba-bind

Filtering to binding assays only (excluding phenotypic assays)
Removing PAINS (pan-assay interference compounds) that show non-specific activity
Providing pre-built validation and test splits for protein-ligand binding prediction
Aggregating the data across assays into combined, easy-to-access files
Providing "compact" versions of each val/test sets to be more accessible to expensive models

Attribution

This work is based on MF-PCBA by David Buterez et al. The original dataset, retrieval scripts, and methodology are preserved in the original-mf-pcba/ directory.

If you use this dataset, please cite the original MF-PCBA paper:

@article{doi:10.1021/acs.jcim.2c01569,
    author = {Buterez, David and Janet, Jon Paul and Kiddle, Steven J. and Li�, Pietro},
    title = {MF-PCBA: Multifidelity High-Throughput Screening Benchmarks for Drug Discovery and Machine Learning},
    journal = {Journal of Chemical Information and Modeling},
    year = {2023},
    doi = {10.1021/acs.jcim.2c01569},
    URL = {https://doi.org/10.1021/acs.jcim.2c01569}
}

Dataset Overview

Data Files

File	Description
`data/mf_pcba_bind_val_full.parquet`	Full validation set with all binders and non-binders
`data/mf_pcba_bind_val_compact.parquet`	Compact validation set (binders + 4x sampled non-binders)
`data/mf_pcba_bind_test_full.parquet`	Full test set with all binders and non-binders
`data/mf_pcba_bind_test_compact.parquet`	Compact test set (binders + 4x sampled non-binders)
`data/mf_pcba_bind_val+test_full.parquet`	Combined val+test full set
`data/mf_pcba_bind_val+test_compact.parquet`	Combined val+test compact set
`data/MF-PCBA-Assay-Metadata.csv`	Curated metadata for all assays including protein sequences

Columns

Each parquet file contains:

CID: PubChem Compound ID
smiles: Molecular SMILES string
binds: Binary label (1 = binder, 0 = non-binder)
protein_name: Target protein name
protein_category: A rough categorization of the protein
protein_accession: Protein accession number
amino_acid_sequence: Full protein sequence
AID: PubChem Assay ID

Label Definitions

Binders (binds=1): Compounds marked "Active" in dose-response (DR) confirmatory screening
Non-binders (binds=0): Compounds marked "Inactive" in single-dose (SD) primary screening

PAINS Filtering

PAINS (Pan-Assay Interference Compounds) are filtered out using RDKit's FilterCatalog. These are compounds that tend to show activity across many assays due to non-specific mechanisms (e.g., aggregation, redox cycling, fluorescence interference) rather than genuine target binding.

Scripts

`scripts/build_val_test_sets.py`

Builds the validation and test parquet files from retrieved MF-PCBA data:

Reads manually reviewed and curated assay metadata from data/MF-PCBA-Assay-Metadata.csv
Filters to binding assays only (excludes phenotypic assays)
Extracts binders (DR active) and non-binders (SD inactive)
Removes PAINS compounds using RDKit's FilterCatalog
Adds protein sequence information to each compound
Creates full and compact versions of validation, test, and combined sets

Requirements: pandas, numpy, pyarrow, rdkit

Usage:

# First, retrieve the raw MF-PCBA data using scripts in original-mf-pcba/
# Then run:
python scripts/build_val_test_sets.py

Original MF-PCBA

The original-mf-pcba/ directory contains the original MF-PCBA retrieval code and scripts. See original-mf-pcba/README-original.md for details on downloading and processing the raw PubChem data.

License

MIT License - see LICENSE