Introduction to Computer-driven Drug Discovery

Introduction to Computer-driven Drug Discovery#

Author: Dr Xavier Chee Updated: 5 January, 2026

Technical Acknowledgement: The interactive visualizations, widgets, and associated Python code used in this course material were developed with the assistance of AI coding assistants, specifically Google Gemini 3 and Anthropic Claude.

Welcome#

Welcome to this interactive learning book! This comprehensive guide contains 20 chapters covering essential topics in basic biology and chemistry for Drug Discovery. This book contains the pre-requisite knowledge for the PHM5013 Precision Drug Discovery and Pharmacogenomics course

How to Use This Book#

This book is built with Jupyter Book and supports interactive code execution through Thebe. You can:

  • Read the content like a traditional textbook

  • Execute code cells directly in your browser

  • Interact with the widgets and animations

Table of Contents#

Chapter 1.1: Protein Structure Hierarchy Primary
Chapter 1.2: Intrinsically Disordered Proteins
Chapter 1.3: Protein Families and Classification
Chapter 1.4: Domain Architecture and Motifs
Chapter 1.5: Protein Flexibility and Conformational Changes
Chapter 2.1: Atoms and Chemical Bonding
Chapter 2.2: Common Functional Groups in Drug Molecules
Chapter 2.3: Aromaticity and Resonance
Chapter 2.4: Hybridization and Molecular Geometry
Chapter 2.5: Molecular Conformations and Rotatable Bonds
Chapter 2.6: Stereochemistry Chirality and Isomerism
Chapter 2.7: Configurational and Conformational Isomers
Chapter 2.8: Physicochemical Properties Logp Pka Solubility
Chapter 2.9: Hydrogen Bond Donors and Acceptors
Chapter 2.10: Hydrogen Bonding in Protein Ligand Interactions
Chapter 2.11: Van Der Waals Forces and Hydrophobic Effects
Chapter 2.12: Electrostatic Interactions and Pi Interactions
Chapter 3.1: Basic Concepts of Enthalpy and Entropy
Chapter 3.2: Gibbs Free Energy and Spontaneity

Getting Started#

To begin your learning journey, click on any chapter above or use the navigation sidebar on the left.

Interactive Features#

This book includes interactive features powered by Thebe:

  • Click the Live Code button at the top of any page to activate interactive mode

  • Edit and run code cells to see immediate results

  • Experiment with different inputs and parameters

Prerequisites#

This book assumes:

  • Basic computer literacy

  • Willingness to learn and experiment

Happy Learning!

Contents