Global distance test

The GDT score is calculated as the largest set of amino acid residues' alpha carbon atoms in the model structure falling within a defined distance cutoff of their position in the experimental structure, after iteratively superimposing the two structures. By the original design the GDT algorithm calculates 20 GDT scores, i.e. for each of 20 consecutive distance cutoffs (0.5 Å, 1.0 Å, 1.5 Å, ... 10.0 Å). ==Variations and extensions==

The original GDT_TS is calculated based on the superimpositions and GDT scores produced by the Local-Global Alignment (LGA) program. CASP8 defined a new "TR score", which is GDT_TS minus a penalty for residues clustered too close, meant to penalize steric clashes in the predicted structure, sometimes to game the cutoff measure of GDT. The primary GDT assessment uses only the alpha carbon atoms. To apply superposition‐based scoring to the amino acid residue side chains, a GDT‐like score called "global distance calculation for sidechains" (GDC_sc) was designed and implemented within the LGA program in 2008. GDT scores are generally computed with respect to a single reference structure. In some cases, structural models with lower GDT scores to a reference structure determined by protein NMR are nevertheless better fits to the underlying experimental data. Methods have been developed to estimate the uncertainty of GDT scores due to protein flexibility and uncertainty in the reference structure. ==See also==