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<p>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.<br>
<br>
Now, thanks to ColabFold, anyone can submit a sequence and get a
free AlphaFold2 structure prediction. Its easy! Here are
instructions:<br>
<br>
<a class="moz-txt-link-freetext" href="https://proteopedia.org/w/How_to_predict_structures_with_AlphaFold">https://proteopedia.org/w/How_to_predict_structures_with_AlphaFold</a><br>
<br>
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<br>
<br>
<a class="moz-txt-link-freetext" href="http://bioinformatics.org/firstglance/fgij">http://bioinformatics.org/firstglance/fgij</a><br>
<br>
Snapshot of Alphafold2 Colab prediction displayed in FirstGlance
colored by estimated reliability per residue:
<a class="moz-txt-link-freetext" href="https://bioinformatics.org/molvis/images/firstglance-with-alphafold.png">https://bioinformatics.org/molvis/images/firstglance-with-alphafold.png</a><br>
<br>
Examples of AlphaFold2 Colab predictions ready to view instantly
in FirstGlance:
<a class="moz-txt-link-freetext" href="https://bioinformatics.org/firstglance/fgij/versions.htm">https://bioinformatics.org/firstglance/fgij/versions.htm</a><br>
<br>
* ColabFold - Making protein folding accessible to all by M.
Mirdita, S. Ovchinnikov, & M. Steinegger:
<a class="moz-txt-link-freetext" href="https://www.biorxiv.org/content/10.1101/2021.08.15.456425v1">https://www.biorxiv.org/content/10.1101/2021.08.15.456425v1</a><br>
* More about AlphaFold: <a class="moz-txt-link-freetext" href="https://proteopedia.org/w/Alphafold">https://proteopedia.org/w/Alphafold</a><br>
* About the 2020 CASP blind competition:
<a class="moz-txt-link-freetext" href="https://proteopedia.org/w/Theoretical_models">https://proteopedia.org/w/Theoretical_models</a><br>
* AlphaFold Database of several hundred thousand predictions:
<a class="moz-txt-link-freetext" href="https://alphafold.ebi.ac.uk/">https://alphafold.ebi.ac.uk/</a><br>
* Official Deepmind AlphaFold blog post:
<a class="moz-txt-link-freetext" href="https://deepmind.com/blog/article/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology">https://deepmind.com/blog/article/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology</a></p>
<p>-Eric Martz<br>
</p>
<div class="moz-signature"
signature-switch-id="a4e4a06d-98be-4305-8faf-93c6b03ef414">Eric
Martz, Professor Emeritus, Dept Microbiology (he/him/his)<br>
University of Massachusetts, Amherst MA US<br>
<a href="http://Martz.MolviZ.Org">Martz.MolviZ.Org</a>
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