Datasets:

ivanovaml
/

G9a_onlyInhibitors_targetEfficacy_basic

+---
+license: apache-2.0
+tags:
+- chemistry
+- biology
+- medical
+size_categories:
+- 10K<n<100K
+---
+# Dataset Purpose
+The dataset
+G9a_onlyInhibitors_targetEfficacy_basic 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
+# 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 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
+Dataset Details
+Rows: 26,790
+- Column 1: CID (compounds` PubChem identifiers)
+- Column 2: SID (substances` PubChem identifiers)
+- Column 3: Efficacy of the G9a inhibition (target)
+- Column 4: SMILES - Simplified Molecular-Input Line-Entry System that is a line notation describes the three-dimensional
+structure of Chemical formulations was used to calculate the attribute Similarity described below
+- Column 5: MW - Molecular weight is calculated as the sum of the mass of each constituent atom
+multiplied by the number of atoms of that element in the molecular formula.
+- Column 6: MF - Molecular formulas contain information about the type of atoms and their number in molecules. These data were
+used to calculate the mass fraction and the relative fraction of atoms in the molecule for each compound under
+consideration
+- Column 7: TPSA -The topological polar surface area is an estimate of the polar surface area of a molecule, computed as
+the surface sum over polar atoms in the molecule
+- Column 8: XLogP3 is a predicted octanol-water partition coefficient measuring the hydrophilicity or hydrophobicity of a
+molecule
+- Column 9: HAC - Heavy Atom Count is the number of heavy atoms (i.e., non-hydrogen atoms) in the given compound.
+- Column 10: HBDC -  Hydrogen Bond Donor Count in the compound
+- Column 11: HBAC - Hydrogen Bond Acceptor Count in the compound
+- Column 12: RBC - Rotatable Bond Count is defined as any single-order non-ring bond, where atoms on either side of the bond are
+in turn bound to nonterminal heavy (i.e., non-hydrogen) atoms.  That is, where rotation around the bond axis changes the overall shape of the molecule and generates conformers
+- Column 13: CBUC - Covalently Bonded Unit Count is the number of groups of atoms connected by covalent bonds
+- Column 14: MMX6 - 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 carbon atoms only (given that carbon atoms create the "skeleton" of the organic compound)
+- Column 15: 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 16: SX6 - Skewness of the atom coordinate distribution. The feature
+derived from 2D coordinates related to the distribution of the atoms
+along the x axis. The values of skewness were calculated for the carbon atoms only
+- Column 17: SX - Skewness of the atom coordinate distribution. The feature
+derived from 2D coordinates related to the distribution of the atoms
+along the x axis. The values of skewness were calculated for all atoms
+- Column 18: MMY6 -  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 y axis performed for carbon atoms only (given that carbon atoms create the "skeleton" of the organic compound)
+- Column 19: MMY - 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 y axis performed for all atoms
+- Column 20: SY6 - Skewness of the atom coordinate distribution. The feature
+derived from 2D coordinates related to the distribution of the atoms
+along the y axis. The values of skewness were calculated for the carbon atoms only
+- Column 21: SY - Skewness of the atom coordinate distribution. The feature
+derived from 2D coordinates related to the distribution of the atoms
+along the y axis. The values of skewness were calculated for all atoms
+- Column 22: Volume_1 - Hypothetical volumes of the molecules Type 1 calculated based on the 2D coordinates that carry information about the isomers. Since atoms, respectively molecules are not flat, the 2D data of the atomic coordinates of the substances were used to obtain a hypothetical 3D volume of the compounds. These computations were based on the previously obtained min-max values of the atoms' coordinates.
+- Column 23: Volume_2 - Hypothetical volumes of the molecules Type 2 calculated using the already computed skewness of the atoms` coordinates. Since atoms, respectively molecules are not flat, the 2D data of the atomic coordinates of the substances were used to obtain a hypothetical 3D volume of the compounds. These computations were based on the previously computed skewness of the atoms` coordinates
+- Column 24: MMX6_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 carbon atoms only (given that carbon atoms create the "skeleton" of the organic compound)
+- Column 25: 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 26: SX6_3D - Skewness derived from the 3D coordinates related to the distribution of C atoms along the z axis.
+- Column 27: SX_3D - Skewness derived from the 3D coordinates related to the distribution of all atoms along the x axis.
+- Column 28: 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 29: 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 30: SY6_3D - Skewness derived from the 3D coordinates related to the distribution of C atoms along the y axis.
+- Column 31: SY_3D - Skewness derived from the 3D coordinates related to the distribution of all atoms along the y axis.
+- Column 32: MMZ6_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 z  axis performed for carbon atoms only (given that carbon atoms create the "skeleton" of the organic compound)
+- Column 33: MMZ_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 z axis performed for all atoms.
+- Column 34: SZ6_3D - Skewness derived from the 3D coordinates related to the distribution of C atoms along the z axis.
+- Column 35: SZ_3D - Skewness derived from 3D coordinates related to the distribution of all atoms along the z axis.
+- Column 36: Volume_1_3D - Hypothetical volume based on 3D coordinates of the atoms` coordinates.
+- Column 37: 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 38: 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 39: 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 40: 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 41: H_relative -  The relative proportion of the H atom in the molecules of the considered compounds is a feature that carry information about the proportion of the number of H atoms to the total number of atoms in the given compound.
+- Column 42: 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 43: S_relative -  The relative proportion of the S atom in the molecules of the considered compounds is a feature that carry information about the proportion of the number of S atoms to the total number of atoms in the given compound.
+- Column 44: N_relative -  The relative proportion of the N atom in the molecules of the considered compounds is a feature that carry information about the proportion of the number of N atoms to the total number of atoms in the given compound.
+- Column 45: Br_relative -  The relative proportion of the Br atom in the molecules of the considered compounds is a feature that carry information about the proportion of the number of Br atoms to the total number of atoms in the given compound.
+- Column 46: Cl_relative - The relative proportion of the Cl atom in the molecules of the considered compounds is a feature that carry information about the proportion of the number of Cl atoms to the total number of atoms in the given compound.
+- Column 47: F_relative -  The relative proportion of the F atom in the molecules of the considered compounds is a feature that carry information about the proportion of the number of F atoms to the total number of atoms in the given compound.
+- Column 48: C - The mass proportion of the C 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 49: H - The mass proportion of the H 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 50: O - The mass proportion of the O 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 51: 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 52: N - The mass proportion of the N 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 53: Br - The mass proportion of the Br 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 54: Cl  - The mass proportion of the Cl 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 55: F - The mass proportion of the F 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 56: C_rel_2D - The size ratio of the molecules based on 2D C atoms` coordinates
+- Column 57: allAtoms_rel_2D - The size ratio of the molecules based on 2D atoms` coordinates
+- Column 58: C_rel_XY_3D - The size ratio of the molecules based on 2D C atoms` coordinates along the X and Y axes
+- Column 59: allAtoms_rel_XY_3D - The size ratio of the molecules based on 3D atoms` coordinates along the X and Y axes
+- Column 60:	C_rel_XZ_3D - The size ratio of the molecules based on 2D C atoms` coordinates along the X and Z axes
+- Column 61:	allAtoms_rel_XZ_3D - The size ratio of the molecules based on 3D atoms` coordinates  along the X and Z axes
+- Column 62:	C_rel_YZ_3D - The size ratio of the molecules based on 2D C atoms` coordinates along the Y and Z axes
+- Column 63:	allAtoms_rel_YZ_3D - The size ratio of the molecules based on 3D atoms` coordinates  along the Y and Z axes
+- Column 64: 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.