README.md

metadata

license: cc-by-4.0
task_categories:
  - tabular-classification
tags:
  - chemistry
  - drug-discovery
  - pubchem
  - bioassay
  - smiles
  - rdkit

Simeonov2008: PubChem Bioassay Active Compounds

Overview

Active compounds from PubChem qHTS bioassay screenings (AIDs: 587, 588, 590, 591, 592, 593, 594) based on Simeonov et al. (2008). SMILES were sanitized using RDKit MolStandardize.

Metric	Value
Total rows	7109
Unique compounds	6743
Assays	6

Quick Start

from datasets import load_dataset

# Load dataset
dataset = load_dataset("jpraise/Simeonov2008")

# Get full data as DataFrame
df = dataset['full'].to_pandas()
print(df.head())

Data Fields

Column	Description
AID	PubChem Assay ID
CID	PubChem Compound ID
SMILES	Original SMILES from PubChem
InChI	IUPAC InChI identifier
InChIKey	Hashed InChI key
SMILES_sanitized	Standardized SMILES via RDKit

Assays

AID	Link
587	PubChem
588	PubChem
590	PubChem
591	PubChem
592	PubChem
593	PubChem
594	PubChem

SMILES Sanitization

RDKit MolStandardize pipeline:

1. LargestFragmentChooser - Remove salts/counterions
2. Normalizer - Standardize functional groups
3. Uncharger - Neutralize charges
4. TautomerEnumerator - Canonicalize tautomers

Citation

@article{simeonov2008,
  title={Fluorescence spectroscopic profiling of compound libraries},
  author={Simeonov, Anton and Jadhav, Ajit and Thomas, Craig J and others},
  journal={Journal of Medicinal Chemistry},
  volume={51},
  number={8},
  pages={2363--2371},
  year={2008},
  doi={10.1021/jm701301m}
}

License

CC-BY-4.0. Source data from PubChem (public domain).