AlphaFold2 examples from CASP 14: Difference between revisions
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===Second Best Prediction for ORF8=== | ===Second Best Prediction for ORF8=== | ||
In CASP 14, 70 research groups and 42 automated servers predicted structures for ORF8. The median GDT_TS score for all 112 predictions was 26. AlphaFold2 made the best prediction (GDT_TS 87). <scene name='87/875686/Second_best_orf8_imf/1'>The second best prediction was by the group of Xian Ming Pan</scene>, with GDT_TS 43 (see TABLE above). The fold and topology were predicted correctly, but the '''details are far less accurate''' than those in AlphaFold2's prediction. The 2nd best prediction has '''no disulfide bonds'''. | In CASP 14, 70 research groups and 42 automated servers predicted structures for ORF8. The median GDT_TS score for all 112 predictions was 26. AlphaFold2 made the best prediction (GDT_TS 87). <scene name='87/875686/Second_best_orf8_imf/1'>The second best prediction was by the group of Xian Ming Pan</scene>, with GDT_TS 43 (see TABLE above). The fold and topology were predicted correctly, but the '''details are far less accurate''' than those in AlphaFold2's prediction. The 2nd best prediction has '''no disulfide bonds'''. The '''salt bridge''' Arg86:Asp98 is correctly predicted, along with two incorrectly predicted salt bridges. | ||
===Third Best Prediction for ORF8=== | ===Third Best Prediction for ORF8=== | ||
The third best prediction for ORF8 was by the Perez Lab, with GDT_TS 33 (see TABLE above). It '''correctly predicted the parallel beta strands formed by the amino and carboxy terminal ends of the chain'''. <scene name='87/875686/3rd_best_orf8/1'>When the 2-stranded parallel beta strands formed by the ends of the chains are aligned, the remainder aligns poorly</scene>. This prediction has '''no disulfide bonds'''. | The third best prediction for ORF8 was by the Perez Lab, with GDT_TS 33 (see TABLE above). It '''correctly predicted the parallel beta strands formed by the amino and carboxy terminal ends of the chain'''. <scene name='87/875686/3rd_best_orf8/1'>When the 2-stranded parallel beta strands formed by the ends of the chains are aligned, the remainder aligns poorly</scene>. This prediction has '''no disulfide bonds'''. The '''salt bridge''' Arg86:Asp98 is correctly predicted, along with two incorrectly predicted salt bridges. | ||
===Top Prediction by an Automated Server=== | ===Top Prediction by an Automated Server=== | ||
Among predictions by automated servers for all ~100 CASP 14 targets, the top ranking server was QUARK from the Yang Zhang group (Univ. Michigan). For ORF8, the Zhang-TBM server made the best server prediction with a '''GDT_TS of 27'''. (The prediction by QUARK was almost as good, GDT_TS 26.) The prediction has the '''two chain termini not parallel, and the amino terminus is not a beta strand''', differing in both respects from the X-ray model. Also, '''no disulfide bonds''' are predicted. The structural alignment is very poor and is not shown. | Among predictions by automated servers for all ~100 CASP 14 targets, the top ranking server was QUARK from the Yang Zhang group (Univ. Michigan). For ORF8, the Zhang-TBM server made the best server prediction with a '''GDT_TS of 27'''. (The prediction by QUARK was almost as good, GDT_TS 26.) The prediction has the '''two chain termini not parallel, and the amino terminus is not a beta strand''', differing in both respects from the X-ray model. Also, '''no disulfide bonds''' are predicted. The structural alignment is very poor and is not shown. The '''salt bridge''' Arg86:Asp98 is correctly predicted, along with two incorrectly predicted salt bridges. | ||
===Baker Rosetta Server Prediction for ORF8=== | ===Baker Rosetta Server Prediction for ORF8=== | ||
Among predictions for all ~100 CASP 14 targets, the group of David Baker [https://predictioncenter.org/casp14/zscores_final.cgi ranked second]. The Rosetta Server of the Baker group ranked 18th overall, but was the 4th ranked server<ref name="serverranks">For all targets in CASP 14, the top two servers were QUARK and Zhang-server (which were not significantly different at a Z-score sum of 62.9), followed by Zhang-CEthreader (55.9) and BAKER-ROSETTASERVER (55.3).</ref>. [https://predictioncenter.org/casp14/results.cgi?view=tables&target=T1064-D1&model=1&groups_id= For ORF8, the Rosetta Server prediction GDT_TS was 26], a bit better than the median of 23. The Rosetta Server's prediction for ORF8 has '''the two termini far apart''' (Cα 13 Å or farther apart), a substantial difference from the X-ray structure (Cα mostly ~5 Å apart). It predicts '''two disulfide bonds, but neither matches''' the pairs of Cys residues in the actual disulfide bonds. The structural alignment is very poor and is not shown. | Among predictions for all ~100 CASP 14 targets, the group of David Baker [https://predictioncenter.org/casp14/zscores_final.cgi ranked second]. The Rosetta Server of the Baker group ranked 18th overall, but was the 4th ranked server<ref name="serverranks">For all targets in CASP 14, the top two servers were QUARK and Zhang-server (which were not significantly different at a Z-score sum of 62.9), followed by Zhang-CEthreader (55.9) and BAKER-ROSETTASERVER (55.3).</ref>. [https://predictioncenter.org/casp14/results.cgi?view=tables&target=T1064-D1&model=1&groups_id= For ORF8, the Rosetta Server prediction GDT_TS was 26], a bit better than the median of 23. The Rosetta Server's prediction for ORF8 has '''the two termini far apart''' (Cα 13 Å or farther apart), a substantial difference from the X-ray structure (Cα mostly ~5 Å apart). It predicts '''two disulfide bonds, but neither matches''' the pairs of Cys residues in the actual disulfide bonds. The '''salt bridge''' Arg86:Asp98 is correctly predicted, along with one incorrectly predicted salt bridge. The structural alignment is very poor and is not shown. | ||
</StructureSection> | </StructureSection> | ||
Revision as of 00:58, 26 February 2021
This page is under construction. Eric Martz 01:03, 22 February 2021 (UTC)
Prediction of protein structures from amino acid sequences, homology modeling, has been extremely challenging. In 2020, breakthrough success was achieved by AlphaFold2[1], a project of DeepMind. For an overview of this breakthrough, documented by the bi-annual prediction competition empirical models, please see 7jtl. Below are illustrated some examples of predictions from that competition.
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References
- ↑ Senior AW, Evans R, Jumper J, Kirkpatrick J, Sifre L, Green T, Qin C, Zidek A, Nelson AWR, Bridgland A, Penedones H, Petersen S, Simonyan K, Crossan S, Kohli P, Jones DT, Silver D, Kavukcuoglu K, Hassabis D. Improved protein structure prediction using potentials from deep learning. Nature. 2020 Jan;577(7792):706-710. doi: 10.1038/s41586-019-1923-7. Epub 2020 Jan, 15. PMID:31942072 doi:https://dx.doi.org/10.1038/s41586-019-1923-7
