ivanovaml/G9a_onlyInhibitors_targetEfficacy_noSkew

Dataset Purpose

The dataset G9a_onlyInhibitors_targetEfficacy_noSkew had been used in the study "Targeting neurodegeneration: three machine learning methods for G9a inhibitors discovery using PubChem and scikit-learn" https://doi.org/10.1007/s10822-025-00642-z as the Dataset_5.

Info

This dataset is from samples used in the PubChem AID 504332 bioassay "qHTS Assay for Inhibitors of Histone Lysine Methyltransferase G9a", https://pubchem.ncbi.nlm.nih.gov/bioassay/504332

Some of the features in this datasets had been engineered during the study "Application of machine learning for predicting G9a inhibitors" https://doi.org/10.1039/d4dd00101j

Source code

Datasets: https://github.com/articlesmli/G9a_Inhibitors_efficacy/tree/main/1.G9a_inhibitor_efficacy_magnitude_ML_model

Feature engineering: https://github.com/articlesmli/G9a_clsf/blob/main/with%20solubility/data_sets_generation_with_SMOTE.ipynb

Dataset Details

Rows: 3,890

Columns: 22

A note: Remove the column "Unnamed: 0".

• Column 1: O_relative - The relative proportion of the O atom in the molecules of the considered compounds is a feature that carry information about the proportion of the number of O atoms to the total number of atoms in the given compound.
• Column 2: Similarity - The feature is based on the comparison between SMILES of the compounds and Lysine. Lysine was chosen because the methylation has been performed in the Lysine residue. The “Similarity” feature was generated using the toolkit for cheminformatics RDKit‘s packages.
• Column 3: S - The mass proportion of the S atom in the molecules of the considered compound calculated as the proportion of the mass of all identical atoms in the molecule to the mass of all atoms in the molecule of the given compound
• Column 4: C_rel_2D - The size ratio of the molecules based on 2D C atoms` coordinates.
• Column 5: allAtoms_rel_2D - The size ratio of the molecules based on 2D atoms` coordinates
• Column 6: C_rel_XY_3D - The size ratio of the molecules based on 2D C atoms` coordinates along the X and Y axes
• Column 7: allAtoms_rel_XY_3D - The size ratio of the molecules based on 3D atoms` coordinates along the X and
• Column 8: MMY_3D - Difference between Min and Max of the atoms' coordinates of the compounds where the minima of the 3D coordinates of the compound was subtracted from the maxima along the y axis performed for all atoms.
• Column 9: CBUC - Covalently Bonded Unit Count is the number of groups of atoms connected by covalent bonds
• Column 10: mean_C**SX6_S - Mean value of the mass proportion of the carbon atoms raised to a power equal to Carbon atoms chain skewness.
• Column 11: mean_H**SX6_S - Mean value of the mass proportion of the Hydrogen atoms raised to a power equal to the molecule skewness along the 3D axes.
• Column 12: C_rel**MMZ6_3D - the relative ratio of Carbon atoms raised to a power equal to the length of the carbon chain of the compound along the 3D Z axis.
• Column 13: MMX_3D - Difference between Min and Max of the atoms' coordinates of the compounds where the minima of the 3D coordinates of the compound was subtracted from the maxima along the x axis performed for all atoms.
• Column 14: YZ_3D_volume - Hypothetical volume based on the skewness and the difference of min and max derived from the 3D coordinates: an YZ variant.
• Column 15: XY_3D_volume - Hypothetical volume based on the skewness and the difference of min and max derived from the 3D coordinates: an XY variant.
• Column 16: XZ_3D_volume - Hypothetical volume based on the skewness and the difference of min and max derived from the 3D coordinates: an XZ variant.
• Column 17: MMY6_3D - Difference between Min and Max of the atoms' coordinates of the compounds where the minima of the 3D coordinates of the compound was subtracted from the maxima along the Y axis performed for carbon atoms only (given that carbon atoms create the "skeleton" of the organic compound).
• Column 18: MMX - Difference between Min and Max of the atoms' coordinates of the compounds. Based on the PubChem database, in other to distinguish the isomers from each other, the minima of the 2D coordinates of the substances were subtracted from the maxima along the x axis performed for all atoms.
• Column 19: C_relative - The relative proportion of the C atom in the molecules of the considered compounds is a feature that carry information about the proportion of the number of C atoms to the total number of atoms in the given compound.
• Column 20: HBDC - Hydrogen Bond Donor Count in the compound.
• Column 21: mean_H_rel**MM_3D - Mean value of the relative ratio of Hydrogens atoms raised to a power equal to the length of the molecules of the compound along the 3D axes.
• Column 22: Efficacy of the G9a inhibition (the target).