Calculating GDT TS: Difference between revisions

The ''Global Distance Test - Total Score'' (GDT_TS)<ref name="zemla" /><ref name="gdtcaspshort">[https://predictioncenter.org/casp14/doc/help.html#GDT_TS GDT_TS definition] at the CASP 14 website.</ref><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> is used to quantitate the similarity between a predicted protein structure (or any query protein structure), and a reference structure, which is typically an [[empirical model]]. The sequences of the two structures need not be the same. 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. When the two structures differ in detail, GDT_TS is better at detecting similarities in fold than is the ''Root Mean Square Deviation''. "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> Both tests compare the positions of only the alpha carbon atoms. GDT_TS values range from 0 (a meaningless prediction) to 100 (a perfect prediction). "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>.