AlphaFold2 examples from CASP 14: Difference between revisions
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===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 '''salt bridge''' Arg86:Asp98 is correctly predicted, along with one incorrectly predicted salt bridge. The structural superposition 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 superposition is very poor and is not shown. | ||
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==Phage RNA polymerase T1037== | ==Phage RNA polymerase T1037== | ||
