AlphaFold2 examples from CASP 14: Difference between revisions

[https://predictioncenter.org/casp14/domains_summary.cgi More than 100 domains] were provided as prediction targets in CASP 14. 14 of these were in the most difficult category, ''free modeling'' ("FM"), meaning that no informative [[homology modeling]] templates existed. For 8 of these (57%), AlphaFold2's predictions achieved [[Theoretical_modeling#CASP_14_Global_Distance_Test_Results|GDT_TS scores]] of 87-93 (median 88.5). For those 8, GDT_TS of the second best predictions were 43-76 (median 66). Two cases will be analyzed below. <u>First</u>, SARS-CoV-2 ORF8, a 92-residue FM domain where '''AlphaFold2's GDT_TS was 87, and the second best was 43''' (by the group of Xian Ming Pan)<ref name="t1064">For SARS-CoV-2 ORF8, at the [https://predictioncenter.org/casp14/results.cgi?view=tb-sel CASP 14 Table Browser], check T1064-D1 and press ''Show Results''.</ref>. Inspiration for this case came from the discussion by Ribiera<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>. The <u>second</u> case analyzed below was the longest domain in the FM category, 404 residues. AlphaFold2 achieved GDT_TS of 88, and the second best prediction, 63 (by Seok-refine).