Unit 8: RNA Structure Prediction

Material

• slides

• lecture notes

• Video 8-1 (2026-01-29): Noncoding RNA

• Video 8-2 (2026-01-29): RNA secondary structure

• Video 8-3 (2026-01-29): Pseudoknot-free secondary structures, Nussinov algorithm

• Video 8-4 (2026-01-29): Refined energy model, Zuker algorithm

• Video 8-5 (2026-01-29): Grammar based secondary structure prediction

• Video 8-6 (2026-02-05): Probabilistic context-free grammars

• Video 8-6 (2026-02-05): Probabilistic Parsing

• Video 8-6 (2026-02-05): RNA Grammar

Further sources

Further reading on RNA structure and prediction:

• Manolis Kellis et al., Computational Biology - Genomes, Networks, and Evolution, Chapter 10

Background on non-coding RNA:

• Pyle, RNA Structure, Function, and Recognition (online talk series)
  chemical details of what dictates RNA folding and structure
• Munzenmaier, Introduction to Non-Coding RNA
  3D printed models of RNA structures, using kits for teachers

In depth documentary about X-ray crystallography:

• The Royal Institution, Understanding Crystallography

---

Unit 7  ⋅  Syllabus