The Computer Scientist's Guide to Designing mRNA Vaccines

Table of Contents

• 0. Preface
• Part 1: Introduction to mRNA Vaccines
• 1.1. How do Vaccines Work?
• 1.2. How are mRNA Vaccines Different?
• 1.3. Getting to Humans
• 1.4. Why Target Bacteria?
• Part 2: Antigen Selection Pipeline
• 2.1. Overview
• Pipeline
• 2.2.1. Gathering Data
• 2.2.2. Removing Accessory Proteins
• 2.2.3. Homologous Protein Removal
• 2.2.4. Localization Screening
• 2.2.5. Essential proteins and virulence factors
• 2.3. Pipeline Recap
• 2.4. Manual Review
• 2.5. Pipeline Alternatives
• Part 3: Sequence Optimization
• 3.1. Why Optimization Is Possible
• 3.2. Nussinov and Zuker
• 3.3. Folding & Minimum Free Energy
• 3.4. The Codon Adaptation Index
• 3.5. LinearFold & LinearDesign