[Proteopedia] Predict protein structure from sequence easily, free!
Eric Martz
emartz at microbio.umass.edu
Sat Oct 23 17:53:45 EDT 2021
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>
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