AlphaFold2 examples from CASP 14: Difference between revisions
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First, SARS-CoV-2 ORF8<ref name="7jtl" />, 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>, the largest difference between 1st and 2nd predictions among the FM targets. It is further unusual because two independently-determined X-ray crystallographic structures were subsequently published. Inspiration for this case came from 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>. | First, SARS-CoV-2 ORF8<ref name="7jtl" />, 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>, the largest difference between 1st and 2nd predictions among the FM targets. It is further unusual because two independently-determined X-ray crystallographic structures were subsequently published. Inspiration for this case came from 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>. | ||
Second, the '''longest domain in the FM category, 404 residues'''. This domain is part of the 2,180-residue RNA polymerase of a bacteriophage, some of whose group members are prevalent in the human gut<ref name="6vr4">PMID: 33208949</ref>. Eight of the CASP 14 FM target domains are parts of this protein, [[6vr4]]. For the 404-residue domain, AlphaFold2 achieved GDT_TS of 88, and the second best prediction, 63 (by Seok-refine). Among the 14 FM targets, the second-longest has 276 residues, the median 132, and the shortest, 92. | Second, the '''longest domain in the FM category, 404 residues'''. This domain is part of the 2,180-residue RNA polymerase of a bacteriophage, some of whose group members are prevalent in the human gut<ref name="6vr4">PMID: 33208949</ref>. Eight of the CASP 14 FM target domains are parts of this protein, [[6vr4]]. For the 404-residue domain T1037, AlphaFold2 achieved GDT_TS of 88, and the second best prediction, 63 (by Seok-refine). Among the 14 FM targets, the second-longest has 276 residues, the median 132, and the shortest, 92. | ||
==SARS-CoV-2 ORF8== | ==SARS-CoV-2 ORF8== | ||