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 [[RMSD|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>.

The accuracies of predictions submitted to the [[CASP|biannual CASP competitions]] are judged largely by GDT_TS. Proteopedia pages using GDT_TS include [[Theoretical models]] and [[AlphaFold2 examples from CASP 14]].

GDT_TS can be calculated with the [http://linum.proteinmodel.org/ AS2TS Server] provided by [http://linum.proteinmodel.org/AS2TS/people/Zemla/ Adam Zemla]<ref name="zemla">PMID: 12824330</ref><ref name="as2ts">PMID: 15980437</ref>. Below are detailed instructions kindly provided by Zemla in March, 2021.

6. Add at the end of the default parameters "-d:4.0". Thus you will submit your job with these parameters:

:(Without this, LGA defaults to 5.0 Å, but CASP uses 4.0.)

 

7. Press the '''START''' button.

In the results for Run 1, you may be interested in the '''RMSD''' and '''Seq_Id''' for the superposition deemed optimal by this server.

The '''LGA_S''' value (range 0 to 100) is a structure similarity score for the number of alpha carbons given under '''N'''. LGA_S values below ~40 indicate that the two structures have different folds. The LGA_S score for our example is 49.46 for 87 alpha carbons, indicating similar folds.