---
jupytext:
  text_representation:
    extension: .md
    format_name: myst
kernelspec:
  display_name: Python 3
  language: python
  name: python3
---

# 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](1.1_protein_structure_hierarchy_primary.ipynb)  
**Chapter 1.2:** [Intrinsically Disordered Proteins](1.2_intrinsically_disordered_proteins.ipynb)  
**Chapter 1.3:** [Protein Families and Classification](1.3_protein_families_and_classification.ipynb)  
**Chapter 1.4:** [Domain Architecture and Motifs](1.4_domain_architecture_and_motifs.ipynb)  
**Chapter 1.5:** [Protein Flexibility and Conformational Changes](1.5_protein_flexibility_and_conformational_changes.ipynb)  
**Chapter 2.1:** [Atoms and Chemical Bonding](2.1_atoms_and_chemical_bonding.ipynb)  
**Chapter 2.2:** [Common Functional Groups in Drug Molecules](2.2_common_functional_groups_in_drug_molecules.ipynb)  
**Chapter 2.3:** [Aromaticity and Resonance](2.3_aromaticity_and_resonance.ipynb)  
**Chapter 2.4:** [Hybridization and Molecular Geometry](2.4_hybridization_and_molecular_geometry.ipynb)  
**Chapter 2.5:** [Molecular Conformations and Rotatable Bonds](2.5_molecular_conformations_and_rotatable_bonds.ipynb)  
**Chapter 2.6:** [Stereochemistry Chirality and Isomerism](2.6_stereochemistry_chirality_and_isomerism.ipynb)  
**Chapter 2.7:** [Configurational and Conformational Isomers](2.7_configurational_and_conformational_isomers.ipynb)  
**Chapter 2.8:** [Physicochemical Properties Logp Pka Solubility](2.8_physicochemical_properties_logp_pka_solubility.ipynb)  
**Chapter 2.9:** [Hydrogen Bond Donors and Acceptors](2.9_hydrogen_bond_donors_and_acceptors.ipynb)  
**Chapter 2.10:** [Hydrogen Bonding in Protein Ligand Interactions](2.10_hydrogen_bonding_in_protein_ligand_interactions.ipynb)  
**Chapter 2.11:** [Van Der Waals Forces and Hydrophobic Effects](2.11_van_der_waals_forces_and_hydrophobic_effects.ipynb)  
**Chapter 2.12:** [Electrostatic Interactions and Pi Interactions](2.12_electrostatic_interactions_and_pi_interactions.ipynb)  
**Chapter 3.1:** [Basic Concepts of Enthalpy and Entropy](3.1_basic_concepts_of_enthalpy_and_entropy.ipynb)  
**Chapter 3.2:** [Gibbs Free Energy and Spontaneity](3.2_gibbs_free_energy_and_spontaneity.ipynb)  


## 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!*