AlphaFold2 examples from CASP 14: Difference between revisions
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===X-ray crystal structure=== | ===X-ray crystal structure=== | ||
The crystallographic structure, not available to the prediction teams during the CASP competition, is [[6vr4]], with [[resolution]] 3.5 Å, and an Rfree "reliability" of "much better than average for this resolution" (according to [[FirstGlance in Jmol]]). The termini of the chain are far apart from each other (~85 Å), and there are no disulfide bonds. | The crystallographic structure, not available to the prediction teams during the CASP competition, is [[6vr4]], with [[resolution]] 3.5 Å, and an Rfree "reliability" of "much better than average for this resolution" (according to [[FirstGlance in Jmol]]). The termini of the chain are far apart from each other (~85 Å), and there are no disulfide bonds. The [[asymmetric unit]] contains 2 chains. The reference structure was taken from '''chain B''' because it has a lower average [[temperature factor]] than chain A. | ||
The CASP 14 target T1037 sequence of 404 residues begins at sequence number 337 and ends at 901, a span of 565 residues. The target sequence is 404 residues because it excludes residues 370-530 (length 161), which form a different domain. <scene name='87/875686/6vr4_b_2180_residues/4'>Here is the full 2,180 residue chain with 337-901 (565 residues) opaque</scene>. Here is <span style="color:#d000d0;"><b>the 404-residue target sequence </b></span> with the <span class="text-gray"><b>intervening domain (excluded from the CASP target)</b> <scene name='87/875686/6vr4_b_2180_residues/5'>highlighted within the full 2,180-residue chain</scene>. | The CASP 14 target T1037 sequence of 404 residues begins at sequence number 337 and ends at 901, a span of 565 residues. The target sequence is 404 residues because it excludes residues 370-530 (length 161), which form a different domain. <scene name='87/875686/6vr4_b_2180_residues/4'>Here is the full 2,180 residue chain with 337-901 (565 residues) opaque</scene>. Here is <span style="color:#d000d0;"><b>the 404-residue target sequence </b></span> with the <span class="text-gray"><b>intervening domain (excluded from the CASP target)</b> <scene name='87/875686/6vr4_b_2180_residues/5'>highlighted within the full 2,180-residue chain</scene>. | ||
<scene name='87/875686/T1037_length_404/1'>The X-ray structure of CASP 14 domain T1037</scene> (length 404 residues) consists of residues 337-369 + 531-901 of [[6vr4]]. It is an <scene name='87/875686/T1037_length_404/2'>alpha/beta domain with secondary structure</scene> <span style="color:#ff0080;font-weight:bold;">45% helices</span>, <span style="color:#ffc800;background-color:black;font-weight:bold;"> 19% beta strands </span>, and 37% loops and turns. The N- and C-termini are 10 Å apart, and there are no cysteines (thus no disulfide bonds). | <scene name='87/875686/T1037_length_404/1'>The X-ray structure of CASP 14 domain T1037</scene> (length 404 residues) consists of residues 337-369 + 531-901 of [[6vr4]] (taken from chain B). It is an <scene name='87/875686/T1037_length_404/2'>alpha/beta domain with secondary structure</scene> <span style="color:#ff0080;font-weight:bold;">45% helices</span>, <span style="color:#ffc800;background-color:black;font-weight:bold;"> 19% beta strands </span>, and 37% loops and turns. The N- and C-termini are 10 Å apart, and there are no cysteines (thus no disulfide bonds). | ||
===AlphaFold2 prediction for T1037=== | ===AlphaFold2 prediction for T1037=== | ||
