Calculating GDT TS: Difference between revisions
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:In the results for Run 1, you may be interested in the '''RMSD''' and '''Seq_Id''' for the superposition deemed optimal by this server. | :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 is a structure similarity score for the number of alpha carbons given under '''N'''. | The '''LGA_S''' value 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. | ||
:Caveat: If the first structure is half the length of the second '''reference''' structure, then the maximum possible LGA score is 50%. On the other hand, if the second structure is half the length of the first one, then the maximum possible LGA score is 100%. In our example, the length of 5a2f_A is 218 amino acids, and the length of the reference structure 7jx6_A is 104. Therefore, a score of 100 is not impossible. | :Caveat: If the first structure is half the length of the second '''reference''' structure, then the maximum possible LGA score is 50%. On the other hand, if the second structure is half the length of the first one, then the maximum possible LGA score is 100%. In our example, the length of 5a2f_A is 218 amino acids, and the length of the reference structure 7jx6_A is 104. Therefore, a score of 100 is not impossible. | ||
