ivanovaml/TDP1_targetsInhibitors_CID_SID_IUPACs_functionalGroups

Purpose of the Dataset

The TDP1_targetsInhibitors_CID_SID_IUPACs_functionalGroups dataset is a part of the study "Leveraging of the IUPAC Names and Machine Learning for Assisting Drug Discovery and Development, demonstrated on the Case of Human Tyrosyl-DNA Phosphodiesterase 1 (TDP1) Inhibitors" https://doi.org/10.48550/arXiv.2503.05591

Dataset Details

This dataset had been leveraged for computations, such as:

• determine the most or least desirable functional group/fragment that would provide an insight for the development of TDP1 inhibitors
• ML models based on IUPAC names broken down to functional names/fragments
• Define the feature importance of the above-mentioned ML model and explore the proportion between active and inactive compounds, which are the first 10 features

Dataset Description

The dataset contains 101,876 rows, each representing a unique small biomolecule sample. The samples are split between 61,471 TDP1 inhibitors and 40,405 non-inhibitors.

It includes 3 columns:

• Column 1: CID (PubChem identifiers of the compounds that are TDP1 inhibitors)
• Column 2: SID (PubChem identifiers of the substances that are TDP1 inhibitors)
• Column 3: target: "1": The molecule is a TDP1 inhibitor; "0": The molecule is not a TDP1 inhibitor.
• Column 4: IUPAC names of the small biomolecules considered in the study.
• Columns 5-5966: Functional groups/fragments of the small biomolecules considered in the study, which are the results of tokenization of IUPAC names.

The PubChem CIDs, SIDs, IULAC names of the considered small biomolecules, and their labels were taken from PubChem AID 686978 provided by the National Institutes of Health, PubChem, "qHTS for Inhibitors of Human Tyrosyl-DNA Phosphodiesterase 1 (TDP1): qHTS in Cells in Absence of CPT" https://pubchem.ncbi.nlm.nih.gov/bioassay/686978 , which contains 61,471 active compounds out of 424,003 small biomolecules.

The inactive samples were reduced to 40,405 samples by merging the dataset above with the dataset of PubChem AID 1996 bioassay https://pubchem.ncbi.nlm.nih.gov/bioassay/1996 "Aqueous Solubility from MLSMR Stock Solutions", on CID, keeping only the common compounds for both bioassays.