1/10 A š§µof resources to learn about AlphaFold (2 and 3).
IMO, the best way to get started with AF2 is "AlphaFold. A practical guide" from the EMBL-EBI. It explains how AF2 works in plain English, without code, and covers key metrics like pLDDT/PAE/etc.
https://www.ebi.ac.uk/training/online/courses/alphafold/
IMO, the best way to get started with AF2 is "AlphaFold. A practical guide" from the EMBL-EBI. It explains how AF2 works in plain English, without code, and covers key metrics like pLDDT/PAE/etc.
https://www.ebi.ac.uk/training/online/courses/alphafold/
Comments
https://2024.igem.wiki/aachen/education
As an introduction, this other video is IMO a really good technical summary without fine details.
https://www.youtube.com/watch?v=nGVFbPKrRWQ&ab_channel=ArxivInsights
https://nature.com/articles/s41592-024-02272-z
This is also a good summary by Mohammed AlQuraishi
https://www.youtube.com/watch?v=ZJSnfaBJC3Q&ab_channel=OpenMolecularSoftwareFoundation
- the structure prediction problem
- AF2 architecture
- AF2 limitations
... with interesting details
https://nazimbouatta.scholars.harvard.edu/lectures
Also, check out also MassiveFold, a pipeline for massive structure prediction
https://www.nature.com/articles/s43588-024-00714-4
https://alphafoldserver.com/guides
To understand the algorithms behind AF3, check out "The Illustrated AlphaFold"
https://elanapearl.github.io/blog/2024/the-illustrated-alphafold/
https://rcsb.org/news/feature/646e671b1d621d75127a7a52
Also "How to Create a Protein" by Leo Castorina is a good tutorial
https://github.com/universvm/how_to_create_a_protein
AFDB
https://alphafold.ebi.ac.uk
AFDB-clusters
https://afdb-cluster.steineggerlab.workers.dev
ESMAtlas
https://esmatlas.com
PDA
https://pragmaticproteindesign.bio.ed.ac.uk/pda/
BFVD
https://bfvd.steineggerlab.workers.dev
ColabFold DB
https://colabfold.mmseqs.com