Pharmacophore-Driven Kinase Profiling: Application to the PKIS2 Chemogenomic Dataset.

PKIS2 pkis_vrai.xlsx : initial PKIS2 data generation_final_publi.sdf : conformations of compounds in PKIS2. 10 conformations per compound. sorted_output_correlation_kinase_50_percent.csv : correlation between kinase data Pharmacophores and PKIS2 pkis2_3637_unique.txt : 3627 pharmacophores with matching compounds. pkis_vrai_S20_O4_5_all_0_receptor_pharmacophore_count.csv : kinases with the number of matching pharmacophores (NEM threshold value = 0). pkis_vrai_S20_O4_5_all_20_receptor_pharmacophore_count.csv : kinases with the number of matching pharmacophores (NEM threshold value = 20). pkis_vrai_S20_O4_5_all_50_receptor_pharmacophore_count.csv : kinases with the number of matching pharmacophores (NEM threshold value = 50). pkis_vrai_S20_O4_5_all_80_receptor_pharmacophore_count.csv : kinases with the number of matching pharmacophores (NEM threshold value = 80). ChEMBL bioactivity-kinase_2025_01_pki_pIC50_famille_bon_full.csv : kinase data in ChEMBL (Ki and IC50). Analyse_bioactivity-kinase_2025_01_pki_pIC50_famille_bon_full3.csv : number of compounds per kinase along with family, min and max values. fusion_bloc_1.sdf.gz and all the other files (same name between 1 and 9) : Conformations of the compounds associated to kinase ChEMBL data. 10 conformations per compound. KLIFS KLIFS_LIGANDS_SDF2_full_heteroH_with_title_merged_main_rdkit;sdf : KLIFS data for 4731 complexes (sdf format). Pharmacophores and ChEMBL merged_statistics_DDR1_11_unique_full.csv : Kinases matching the DDR1 pharmacophores along with the number of compounds, the family, the mean and max values. merged_statistics_phar_vegfr2_50_5_MMRFS_unique_full.csv : Kinases matching the VEGFR2 pharmacophores along with the number of compounds, the family, the mean and max values. merged_statistics_phar_DDR1_sans_vegfr_3_MMRFS_unique.csv : Kinases matching the DDR1 pharmacophores without VEGFR2 pharmacophores along with the number of compounds, the family, the mean and max values. pourcentage_comparison_with_max_count__phar_DDR1_full_correct.csv : percentage of compounds for each kinase matching the DDR1 pharmacophores. pourcentage_comparison_with_max_count__phar_VEGFR2_full_correct.csv : percentage of compounds for each kinase matching the VEGFR2 pharmacophores. pourcentage_comparison_with_max_count__phar_DDR1_sans_VEGFR2_full_correct.csv : percentage of compounds for each kinase matching the DDR1 pharmacophores (excluding VEGFR2 pharmacophores). Norns norns_2.4_3D.tar.gz : Norns program. Use qmake to generate the Makefile with the Norns.pro file. This is configured for Qt5; for Qt6, replace "5" with "6" (e.g., libQt5Widgets.so → libQt6Widgets.so). In Norns.pro, make sure the path to the Open Babel folder matches your system configuration. The three xml file are provided for the three main operations : DDR1 / VEGFR2 / DDR1 without VEGFR2. Final visualization in Firefox (molecules and pharmacophores) :You need to adjust the configuration via about:config.Set security.fileuri.strict_origin_policy to false. rule_bases_analysis.py : Script for analyzing results (selectivity profiles) from each run. It uses the kinase_famille.csv file during processing.