Reproducibility Archive for Explainable Machine Learning Integrating Quantum Mechanical Descriptors and Matched Molecular Pair Analysis for Scaffold-Generalizable Discovery of Soluble Epoxide Hydrolase Inhibitors.

Zenodo (CERN European Organization for Nuclear Research)

Abstract

This Zenodo repository contains the complete reproducibility archive for the study: "Explainable Machine Learning Integrating Quantum Mechanical Descriptors and Matched Molecular Pair Analysis for Scaffold-Generalizable Discovery of Soluble Epoxide Hydrolase Inhibitors" The archive includes: Machine Learning & Explainable AI (XAI) Raw, curated, and pre-processed datasets Decoy generation scripts and datasets Full descriptor matrices (Mordred and ORCA Quantum Mechanical descriptors) Dimensionality reduction, Sequential Forward Selection (SFS), and PFI feature selection scripts Hyperparameter tuning, model development, and validation notebooks Explainable AI (SHAP and LIME) interpretation data and scripts Matched Molecular Pair Analysis (MMPA) & Virtual Screening MMPA molecular fragmentation and rule extraction Potency-increasing and potency-decreasing structural transformation rules ASINEX screening datasets (full, rule-based filtered, AD-filtered, ML-filtered) MMPA-generated derivatives Screening workflow notebooks and consensus logic scripts Molecular Docking & Sub-Atomic Validation Receptor evaluation files and prepared protein structures Ligand structures AutoDock Vina parameter and configuration files Docking logs, binding energies, and best poses for selected ligands Webtool (IPred-S 1.0) Full Streamlit webtool implementation source code Final trained Random Forest (RF) and Support Vector Machine (SVM) models Standard Scaler parameters and Native Applicability Domain (AD) cutoffs Webtool validation datasets and evaluation scripts This archive is provided to ensure complete transparency and computational reproducibility for peer review.

Authors 4

1. Dileep Kumar

   Manipal Academy of Higher Education

   Affiliation as printed

   Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India

2. Ajwin Joseph Martin

   Manipal Academy of Higher Education

   Affiliation as printed

   Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India

3. Maria Grishina

   South Ural State University

   Affiliation as printed

   Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russian Federation

4. Mohd Shahbaaz Aachen Institute of Inorganic Chemistry

   RWTH Aachen University

   Affiliation as printed

   Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1A, 52074 Aachen, Germany