AlphaFold2 examples from CASP 14: Difference between revisions

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==SARS-CoV-2 ORF8==
==SARS-CoV-2 ORF8==
Following the discussion by Rubiera<ref name="rubiera">[https://www.blopig.com/blog/2020/12/casp14-what-google-deepminds-alphafold-2-really-achieved-and-what-it-means-for-protein-folding-biology-and-bioinformatics/ CASP14: what Google DeepMind’s AlphaFold 2 really achieved, and what it means for protein folding, biology and bioinformatics], a blog post by Carlos Outeir al Rubiera, December 3, 2020.</ref>,
Following the discussion by Rubiera<ref name="rubiera">[https://www.blopig.com/blog/2020/12/casp14-what-google-deepminds-alphafold-2-really-achieved-and-what-it-means-for-protein-folding-biology-and-bioinformatics/ CASP14: what Google DeepMind’s AlphaFold 2 really achieved, and what it means for protein folding, biology and bioinformatics], a blog post by Carlos Outeir al Rubiera, December 3, 2020.</ref>,
our first example will be [[SARS-CoV-2 protein ORF8]], a protein that contributes to virulence in COVID-19<ref name="7jtl">PMID: 33361333</ref>. CASP 14 classified ORF8 as a "free modeling" (FM) target<ref name="casp14domains">[https://predictioncenter.org/casp14/domains_summary.cgi Summary and Classifications of Domains for CASP 14].</ref>, meaning that there were no adequate empirical templates for [[homology modeling]]. Indeed, when the amino acid sequence of ORF8 is submitted to [https://swissmodel.expasy.org/ Swiss Model], it reports the best templates for homology modeling. When the two [[empirical models]] that were not available during CASP 14 are excluded ([[7jtl]] and [[7jx6]]), the best template offered, chain B of [[3afc]], covers only 36% of the length of ORF8 at 13.2% sequence identity. This would be inadequate for constructing a useful model.
our first example will be [[SARS-CoV-2 protein ORF8]], a protein that contributes to virulence in COVID-19<ref name="7jtl">PMID: 33361333</ref>. CASP 14 classified ORF8 as a "free modeling" (FM) target<ref name="casp14domains">[https://predictioncenter.org/casp14/domains_summary.cgi Summary and Classifications of Domains for CASP 14].</ref>, meaning that there were no adequate empirical templates for [[homology modeling]]. This was easily confirmed. When the amino acid sequence of ORF8 is submitted to [https://swissmodel.expasy.org/ Swiss Model], it reports the best templates for homology modeling. When the two [[empirical models]] that were not available during CASP 14 are excluded ([[7jtl]] and [[7jx6]]), the best template offered, chain B of [[3afc]], covers only 36% of the length of ORF8 at 13.2% sequence identity. This would be inadequate for constructing a useful model.


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