AlphaFold2 examples from CASP 14: Difference between revisions
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==SARS-CoV-2 ORF8== | ==SARS-CoV-2 ORF8== | ||
Our first example is [[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 [https://www.uniprot.org/uniprot/P0DTC8 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, with a 4-residue untemplated gap in the sequence alignment. This template would not be adequate for constructing a useful model. | Our first example is [[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, Definitions 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 [https://www.uniprot.org/uniprot/P0DTC8 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, with a 4-residue untemplated gap in the sequence alignment. This template would not be adequate for constructing a useful model. | ||
===X-Ray Structures for ORF8=== | ===X-Ray Structures for ORF8=== | ||
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==GDT_TS Calculations== | ==GDT_TS Calculations== | ||
GDT_TS values for predictions are taken from CASP 14 results. GDT_TS values for 7JTL and 5A2F vs. 7JX6 chain A were calculated using the [http://linum.proteinmodel.org/ AS2TS server] of Adam Zemla<ref name="zemla">PMID: 12824330</ref>. See instructions for [[Calculating GDT_TS]]. CASP 14 reported GDT_TS 86.96 for the AlphaFold2 prediction, while the AS2TS server calculated GDT_TS 86.41 vs. 7jx6 chain A, and 88.59 vs. 7JTL chain A. | GDT_TS values for predictions are taken from CASP 14 results. The reference structure for the CASP 14 GDT_TS values was 92 alpha carbons of 7JTL<ref name="casp14domains" />, since the CASP 14 target had only 92 residues<ref name="casp14domains" />. | ||
GDT_TS values for 7JTL and 5A2F vs. 7JX6 chain A were calculated using the [http://linum.proteinmodel.org/ AS2TS server] of Adam Zemla<ref name="zemla">PMID: 12824330</ref>. See instructions for [[Calculating GDT_TS]]. CASP 14 reported GDT_TS 86.96 for the AlphaFold2 prediction, while the AS2TS server calculated GDT_TS 86.41 vs. 7jx6 chain A, and 88.59 vs. 7JTL chain A. | |||
==References & Notes== | ==References & Notes== | ||
<references /> | <references /> | ||