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Fig. 3 | Algorithms for Molecular Biology

Fig. 3

From: A polynomial time algorithm for computing the area under a GDT curve

Fig. 3

Oversensitivity of GDT_TS. a A four helix bundle-like (toy) protein (dashed grey line) along with two of its, almost identical, models (red and blue). A realistic example of such a target protein (PDB ID: 1JM0A) is shown on the right (b). In this example, we assume that the protein and its models are extended to the right to include 100 or more residues. Note that, if d {1 Å, 2 Å, 4 Å, 8 Å} then the GDT score of the blue model is significantly higher than that of the red model. For instance, if d = 2 Å, then the blue model has the GDT_TS score of about 87.5 since ~50 % all of its residues can be fit at distance ≤1 Å and 100 % under each distance 2, 4 and 8 Å from the corresponding residues in the experimental structure (dashed grey). On the other hand, the GDT_TS score of the red model is only about 75, since only ~50 % of the red model’s residues can be placed under 1 and 2 Å and 100 % under 4 and 8 Å. In fact, no matter how close the red model gets to the blue model, its GDT_TS score will never improve. Note also that the blue and red models have almost identical GDT_A scores, since GDT_A is not sensitive to small coordinate changes

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