Calculating GDT TS: Difference between revisions
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<span class="text-red">'''This page is under construction.''' [[User:Eric Martz|Eric Martz]] 01:18, 5 March 2021 (UTC)</span> | <span class="text-red">'''This page is under construction.''' [[User:Eric Martz|Eric Martz]] 01:18, 5 March 2021 (UTC)</span> | ||
The ''Global Distance Test - Total Score'' (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> is used to quantitate the similarity between a predicted protein structure, and a reference structure, which is typically an [[empirical model]]. 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>. | The ''Global Distance Test - Total Score'' (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> is used to quantitate the similarity between a predicted protein structure, and a reference structure, which is typically an [[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. 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>. | ||
Results 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]]. | Results 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]]. | ||
Revision as of 21:34, 5 March 2021
This page is under construction. Eric Martz 01:18, 5 March 2021 (UTC)
The Global Distance Test - Total Score (GDT_TS)[1][2] is used to quantitate the similarity between a predicted protein structure, and a reference structure, which is typically an 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. 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."[3] 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."[4].
Results of predictions submitted to the 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 free AS2TS Server provided by Adam Zemla. Below are detailed instructions.
ReferencesReferences
- ↑ GDT description at the CASP website.
- ↑ Global distance test at Wikipedia.
- ↑ GDT in the Foldit Wiki.
- ↑ AlphaFold2 @ CASP14: “It feels like one’s child has left home.” by Mohammed AlQuraishi, December 8, 2020.