Learning how to manipulate and visualise protein structures
You’ll find below a short compilation of video extracts found on the Internet that explain various concepts of the AlphaFold algorithm and how to read its outputs. Links towards the complete videos are listed at the bottom of this page.
AlphaFold outputs
Time: 7 mins 30
Concepts: MSA depth & coverage, pLDDT per-residue confidence score, PAE pairwise confidence measure plots
Time: 1 min 30
Concepts: How to read PAE plots for multi-chain predictions
Time: 1 min
Concepts: PAE plot asymmetry
How AlphaFold works?
Time: 12 mins
Concepts: About the protein folding problem, how MSA information is used in AlphaFold2 and how AlphaFold2 generates a model structure
Time: 8 mins
Concepts: Changes and simplifications in AlphaFold3 vs AlphaFold2
Source videos:
- Sami Chaaban’s talk on “AlphaFold: Use and Applications” (MRC-LMB) – https://www.youtube.com/watch?v=yJKfn6rvHmg
- Looking Glass Universe video on “How AlphaFold solves protein folding” – https://www.youtube.com/watch?v=3gSy_yN9YBo
- Looking Glass Universe video on “What’s changed in AlphaFold 3?” – https://www.youtube.com/watch?v=CYncNBMPLLk
The above course material is under CC-BY-SA license.