Recent Advances in Molecular Docking

Dr. Khalid Raza is an Associate Professor at the Department of Computer Science, Jamia Millia Islamia, New Delhi, India, and an Adjunct Professor at UCSI University, Malaysia. He has over 14 years of teaching and research experience and previously served as an ICCR Chair Visiting Professor at Ain Shams University, Egypt. Dr. Raza has published more than 160 peer-reviewed papers and authored/edited over 15 books with Springer, Elsevier, and CRC Press. He serves as Academic Editor of PLoS ONE, BMC Artificial Intelligence, and Guest Editor of npj Precision Oncology, JoVE, and several other journals. Recipient of Clarivate’s (Web of Science) India Excellence Research Citation Award 2025, Dr. Raza is consistently featured in the World’s Top 2% Scientists list (2022–2025). His research focuses on AI, bioinformatics, and health informatics

• Section I: Fundamentals of Molecular Docking1. Fundamentals of Molecular Docking: Concepts, Terminology, Docking Types, and Scoring Functions2. Protein–Ligand Interaction and Binding Site Prediction3. Databases for Molecular Docking: PDB, ChEMBL, ZINC, PubChemSection II: Computational Methods and Workflows4. Molecular Docking Workflows and Pipelines5. Molecular Docking Tools and Their Benchmarking: A Practical Guide for Interdisciplinary Researchers6. Quantum Mechanics and Molecular Mechanics (QM/MM) in Docking7. Molecular Dynamics and Its Integration with Docking StudiesSection III: Advanced Techniques and Integrative Approaches8. Docking Against GPCRs, Ion Channels, and Membrane Proteins9. Ensemble and Multi-Target Docking Approaches for Polypharmacology in Drug Discovery10. Virtual Screening and High-Throughput Docking: Finding Inhibitors Against P-gp Transporter for Treating Hepatocellular Carcinoma (HCC)Section IV: Artificial Intelligence and Machine Learning in Docking11. AI-Driven Molecular Docking: Machine Learning Models, Deep Learning Scoring, and Advanced Docking Frameworks12. TAMARIND: A Unified Framework for Efficient and Accurate Ligand Docking via Deep Learning13. Unifying AI Systems and Elastic Clouds for Scalable CUDA-Based Molecular Docking Using Task Dependency TreesSection V: Applications in Drug Discovery and Therapeutics14. Advances in Structure-Based Drug Design: Principles and Case Studies in Therapeutic Development15. Docking in Cancer, Neurological Disorders, and Infectious Diseases16. Drug Repurposing Using Docking Approaches17. In Silico Study of Phytochemical, Synthetic, and Marine Compounds for Anti-Tubercular (Mycobacterium tuberculosis) Activity18. Structure-Based Drug Designing Using Plant-Derived Compounds: Case Studies19. Molecular Docking Meets Multi-Omics and Systems Biology: A New Era of Precision Therapeutics20. Leveraging Digital Twin Technology with Multi-Omics and Molecular Docking for Precision OncologySection VI: Validation, Platforms, and Future Perspectives21. Challenges in Docking Accuracy and Reproducibility22. Correlation of Computational Molecular Docking Predictions with Experimental Outcomes23. Cloud and HPC Platforms for Molecular Docking and Simulation24. Ethical, Legal, and Regulatory Perspectives in Computational Drug Design

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