by Elvis A. F. Martis
Welcome to the official repository for A Practical Guide To Molecular Docking by Elvis A. F. Martis. This book is a comprehensive guide designed to equip students, researchers, and professionals with the knowledge and tools needed to master molecular docking techniques and their real-world applications in drug discovery. The objective of this textbook is to serve as a handy "user manual" that can explain key steps and points to keep in mind while performing molecular docking. To be Published as Lecture Notes in Chemistry
Molecular docking is a key computational technique used in drug design, structural biology, and bioinformatics. By simulating how molecules interact with each other, molecular docking enables the prediction of binding affinities, which play a crucial role in the development of new therapeutic agents and understanding biological processes.
In this book, we explore the underlying principles of molecular docking, discuss various docking software, and provide hands-on examples to help readers better understand how to apply this knowledge to their research.
- Foundational Principles: Introduction to the principles of molecular docking, including ligand-receptor interactions, docking algorithms, and scoring functions.
- Practical Applications: Insights into how docking is used in drug discovery, virtual screening, and protein-ligand binding studies.
- Case Studies: Real-world examples and case studies to illustrate the application of molecular docking in research and industry.
- Software Tools: Reviews of popular docking software packages, including AutoDock, Dock, and others, with tutorials on how to use them effectively.
- Best Practices: Guidelines on optimising docking simulations, evaluating results, and troubleshooting common issues.
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Chapter 1: Introduction to Structure-based Drug Design
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Chapter 2: Conformational Search Methods for Molecular Docking
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Chapter 3: Scoring Functions
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Chapter 4: Handling Biomacromolecular Structures for Molecular Docking
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Chapter 5: Methods to Identify Binding Site on Proteins
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Chapter 6: Preparation of Small-Molecule Libraries
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Chapter 7: Molecular Docking Methods and Programs
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Chapter 8: Analysing Results from Molecular Docking
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Chapter 9: Molecular Dynamics for Post-Processing of Docking Results
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Chapter 10: Estimating Binding by Free-Energy Methods
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Chapter 11: Communicating Results from Molecular Docking
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Chapter 12: FAIR and Reproducible Reporting of Molecular Docking Results
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Chapter 13: Union of Artificial Intelligence and Molecular Docking
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Chapter 14: Special Methods in Molecular Docking
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Chapter 15: In a Nutshell
This book is ideal for:
- Students: Those studying bioinformatics, computational chemistry, pharmacology, or related fields.
- Researchers: Academics and professionals working in drug discovery, structural biology, or related industries.
- Practitioners: Anyone involved in the development of small molecules or protein-ligand interactions.
Elvis Martis is an experienced researcher in computational biology and drug design. With over 10 years of expertise in molecular docking, he has contributed to numerous publications and projects in the field. His deep understanding of computational techniques and passion for advancing scientific discovery and teaching has motivated him to write this book.
We encourage feedback, suggestions, and contributions! If you're reading the book and would like to share your thoughts, have questions, or need further clarification, feel free to reach out.
- Email: Gmail
- LinkedIn: Elvis Martis