Resources
Main papers
alphafold 1.pdf - first version, kinda shit
main-alphafold-paper.pdf - AlphaFold 2 - the nobel prize winning one
Other resources
Papers
- Supplementary material for AF2 paper - looong as fuck, ton of maths, coding, etc.
- AlphaFold3.pdf - newer AlphaFold 3
- Limitations.pdf - paper on limitations and where AF2 differs from experimental bio.
Explanations
- https://borisburkov.net/2021-12-25-1/ some russian guy's explanation online (some nerd form Russia, no scientist)
- https://shilpa-ananth.github.io/2025-05-25-Alphafold-2-summary/ - another guy's explanation (legit - PI at Oracle AI)
- https://www.youtube.com/@KilianMandon/videos series of YT videos, dunno if legit or not (cited once by the guy above)
Code
- https://github.com/google-deepmind/alphafold Alphafold (2???) repo on github
- https://github.com/aqlaboratory/openfold - Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
- https://github.com/aqlaboratory/openfold-3
- https://github.com/sokrypton/ColabFold - AlphaFold in GoogleColab
Things to play with
- https://alphafoldserver.com/ - official AlphaFold 3 sever, 30 jobs per day
- https://alphafold.ebi.ac.uk/ - AlphaFold DB
Other
- https://www.ebi.ac.uk/training/online/courses/alphafold/ - 3 hour long course on AlphaFold
- https://deepmind.google/blog/alphafold-five-years-of-impact/ - Analysis of 5-year impact of AF2 (by Deepmind)
- https://github.com/microsoft/bioemu - Inference code for scalable emulation of protein equilibrium ensembles with generative deep learning i have no clue either... but its cool , defo not AF but like just maybe cool definitley useless