AlphaFold2 examples from CASP 14: Difference between revisions

The quality of a prediction in CASP is judged, in large part, by the [[Theoretical_models#CASP_14_Global_Distance_Test_Results|Global Distance Test Total Score, GDT_TS]]. AlphaFold2's predicted structure<ref>Download AlphaFold2's predicted structure for ORF8 from [https://predictioncenter.org/casp14/MODELS_PDB/T1064-D1/T1064TS427_1-D1.pdb T1064TS427_1-D1.pdb].</ref> has a '''GDT_TS score of 87'''. (A score of 0 is meaningless, and a score of 100 means perfect agreement with an X-ray crystal structure.) 87 means the model is close to the accuracy of an X-ray crystal structure. The structure predicted by AlphaFold2 is almost as close to the X-ray crystallographic model [[7jx6]] as is the independently-determined X-ray structure [[7jtl]]. AlphaFold2 predicted the positions of 92 amino acids. (CASP 14 excluded residues 48-59, a 12-residue surface loop, from the target residues<ref name="casp14domains" />.) 83 amino acid alpha carbons in the prediction aligned with those in [[7jx6]] with an RMSD of 1.25 Å<ref name="imf" />. When sidechains are included,