Theoretical models: Difference between revisions
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====CASP 14 Global Distance Test Results==== | ====CASP 14 Global Distance Test Results==== | ||
Performance was judged overall, in large part, by the ''global distance test total score'' or [[Calculating GDT TS|GDT_TS]]<ref name="gdtcasp">[https://predictioncenter.org/casp13/doc/LCS_GDT.README GDT description] at the CASP website.</ref><ref name="gdtwikipedia">[https://en.wikipedia.org/wiki/Global_distance_test Global distance test] at Wikipedia.</ref>. GDT_TS values range from 0 (a meaningless prediction) to 100 (a perfect prediction | Performance was judged overall, in large part, by the ''global distance test total score'' or [[Calculating GDT TS|GDT_TS]]<ref name="gdtcasp">[https://predictioncenter.org/casp13/doc/LCS_GDT.README GDT description] at the CASP website.</ref><ref name="gdtwikipedia">[https://en.wikipedia.org/wiki/Global_distance_test Global distance test] at Wikipedia.</ref>. GDT_TS values range from 0 (a meaningless prediction) to 100 (a perfect prediction; see [[Calculating GDT TS]]. "Random predictions give around 20; getting the gross topology right gets one to ~50; accurate topology is usually around 70; and when all the little bits and pieces, including side-chain conformations, are correct, GDT_TS begins to climb above 90."<ref name="alquraishi">[https://moalquraishi.wordpress.com/2020/12/08/alphafold2-casp14-it-feels-like-ones-child-has-left-home/ AlphaFold2 @ CASP14: “It feels like one’s child has left home.”] by Mohammed AlQuraishi, December 8, 2020.</ref>. | ||
A '''GDT_TS value of ~90''' means that the prediction is as close to an [[empirical model]] as would be an independently obtained second empirical model. GDT_TS gives an overall average measure of how close each amino acid in the predicted model is to those in the empirical model, taking into account many different superpositions of the two models. It is less sensitive to outlier regions than is the root mean square deviation (RMSD)<ref name="rmsdwikipedia">[https://en.wikipedia.org/wiki/Root-mean-square_deviation_of_atomic_positions Root mean square deviation] at Wikipedia.</ref>. "RMSD uses the actual distances between alpha carbons, where GDT works with the percentage of alpha carbons that are found within certain cutoff distances of each other."<ref name="gdtfoldit">[https://foldit.fandom.com/wiki/GDT GDT in the Foldit Wiki].</ref> | A '''GDT_TS value of ~90''' means that the prediction is as close to an [[empirical model]] as would be an independently obtained second empirical model. GDT_TS gives an overall average measure of how close each amino acid in the predicted model is to those in the empirical model, taking into account many different superpositions of the two models. It is less sensitive to outlier regions than is the root mean square deviation (RMSD)<ref name="rmsdwikipedia">[https://en.wikipedia.org/wiki/Root-mean-square_deviation_of_atomic_positions Root mean square deviation] at Wikipedia.</ref>. "RMSD uses the actual distances between alpha carbons, where GDT works with the percentage of alpha carbons that are found within certain cutoff distances of each other."<ref name="gdtfoldit">[https://foldit.fandom.com/wiki/GDT GDT in the Foldit Wiki].</ref> | ||