AlphaFold2 examples from CASP 14: Difference between revisions
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===ORF8 Sidechain Accuracy=== | ===ORF8 Sidechain Accuracy=== | ||
Table I gives RMSD values for all atoms, which is one indication of sidechain accuracy. | AlphaFold2's predictions for sidechain positions seem fairly good, while sidechain positions in the 2nd best prediction seem poor. This conclusion is based on three types of observations: | ||
#Table I gives RMSD values for all atoms, which is one indication of sidechain accuracy. | |||
#Prediction of [[salt bridges]] and [[cation-pi interactions]]. | |||
#Visualization of the distributions of charges on the surfaces. | |||
====Salt Bridges and Cation-Pi Interactions==== | |||
*AlphaFold2's prediction was '''correct for 4/5''' interactions, with '''one incorrect''' interaction. | *AlphaFold2's prediction was '''correct for 4/5''' interactions, with '''one incorrect''' interaction. | ||
**AlphaFold2's prediction was '''correct for one of two''' salt bridges, and predicted '''no incorrect''' salt bridges. | **AlphaFold2's prediction was '''correct for one of two''' salt bridges, and predicted '''no incorrect''' salt bridges. | ||
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*The 2nd best prediction has no cation-pi interactions. | *The 2nd best prediction has no cation-pi interactions. | ||
*(AB): The two chains in each X-ray model. | *(AB): The two chains in each X-ray model. | ||
====Visualization of Surface Charge Distributions==== | |||
[[Image:Orf8-casp14-charges.png]] | |||
==References== | ==References== | ||
<references /> | <references /> | ||