[Proteopedia] Predict protein structure from sequence easily, free!

[Eric Martz]

The AlphaFold project of DeepMind (Google) made a dramatic breakthrough 
in 2020. AlphaFold is often able to predict the structure of a protein 
from its sequence so well that the difference between the prediction and 
an X-ray crystallographic structure is as small as the difference 
between two independent X-ray determinations.

Now, thanks to ColabFold, anyone can submit a sequence and get a free 
AlphaFold2 structure prediction. Its easy! Here are instructions:

https://proteopedia.org/w/How_to_predict_structures_with_AlphaFold

Reliability is estimated for each amino acid. FirstGlance in Jmol now 
automatically colors AlphaFold/ColabFold predictions by estimated 
reliability. Upload your predicted PDB file to

http://bioinformatics.org/firstglance/fgij

Snapshot of Alphafold2 Colab prediction displayed in FirstGlance colored 
by estimated reliability per residue: 
https://bioinformatics.org/molvis/images/firstglance-with-alphafold.png

Examples of AlphaFold2 Colab predictions ready to view instantly in 
FirstGlance: https://bioinformatics.org/firstglance/fgij/versions.htm

* ColabFold - Making protein folding accessible to all by M. Mirdita, S. 
Ovchinnikov, & M. Steinegger: 
https://www.biorxiv.org/content/10.1101/2021.08.15.456425v1
* More about AlphaFold: https://proteopedia.org/w/Alphafold
* About the 2020 CASP blind competition: 
https://proteopedia.org/w/Theoretical_models
* AlphaFold Database of several hundred thousand predictions: 
https://alphafold.ebi.ac.uk/
* Official Deepmind AlphaFold blog post: 
https://deepmind.com/blog/article/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology

-Eric Martz

Eric Martz, Professor Emeritus, Dept Microbiology (he/him/his)
University of Massachusetts, Amherst MA US
Martz.MolviZ.Org <http://Martz.MolviZ.Org>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.bioinformatics.org/pipermail/proteopedialist-for-users/attachments/20211023/3f229668/attachment.html>