The global distance test ( GDT ), besides written as GDT_TS to represent “ total score ”, is a quantify of similarity between two protein structures with known amino acidic correspondences ( e.g. identical amino acidic sequences ) but unlike third structures. It is most normally used to compare the results of protein social organization prediction to the experimentally specify structure as measured by x-ray crystallography, protein NMR, or, increasingly, cryoelectron microscopy. The system of measurement was developed by Adam Zemla at Lawrence Livermore National Laboratory and primitively implemented in the Local-Global Alignment ( LGA ) platform. [ 1 ] [ 2 ] It is intended as a more accurate measurement than the common root-mean-square diversion ( RMSD ) metric unit – which is sensitive to outlier regions created, for example, by poor model of individual iteration regions in a structure that is differently sanely accurate. [ 1 ] The conventional GDT_TS sexual conquest is computed over the alpha carbon atoms and is reported as a percentage, ranging from 0 to 100. In general, the higher the GDT_TS grudge, the more closely a exemplar approximates a given reference social organization. GDT_TS measurements are used as major judgment criteria in the production of results from the Critical Assessment of Structure Prediction ( CASP ), a large-scale experiment in the structure prediction community dedicated to assessing current model techniques. [ 1 ] [ 3 ] [ 4 ] The metric unit was first introduced as an evaluation standard in the third iteration of the semiannual experiment ( CASP3 ) in 1998. [ 3 ] Various extensions to the original method acting have been developed ; variations that accounts for the positions of the side chains are known as global distance calculations ( GDC ). [ 5 ]
calculation [edit ]
The GDT score is calculated as the largest stage set of amino acid residues ‘ alpha carbon paper atoms in the model social organization falling within a define distance cutoff of their situation in the experimental social organization, 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 ). [ 2 ] For social organization similarity assessment it is intended to use the GDT scores from several cutoff distances, and scores generally increase with increasing cutoff. A tableland in this increase may indicate an extreme deviation between the experimental and predict structures, such that no extra atoms are included in any shortcut of a reasonable distance. The conventional GDT_TS sum grudge in CASP is the average result of cutoffs at 1, 2, 4, and 8 Å. [ 1 ] [ 6 ] [ 7 ]
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Variations and extensions [edit ]
The master GDT_TS is calculated based on the superimpositions and GDT scores produced by the Local-Global Alignment ( LGA ) plan. [ 1 ] A “ high accuracy ” interpretation called GDT_HA is computed by choice of smaller cutoff distances ( half the size of GDT_TS ) and thus more heavily penalizes larger deviations from the reference structure. It was used in the high accuracy class of CASP7. [ 8 ] CASP8 defined a new “ TR score ”, which is GDT_TS minus a penalty for residues clustered excessively close, entail to penalize steric clashes in the bode structure, sometimes to crippled the shortcut measure of GDT. [ 9 ] [ 10 ] The chief GDT appraisal uses merely the alpha carbon atoms. To apply superposition‐based score to the amino acid remainder side chains, a GDT‐like score called “ global distance calculation for sidechains ” ( GDC_sc ) was designed and implemented within the LGA platform in 2008. [ 1 ] [ 5 ] rather of comparing remainder positions on the basis of alpha carbons, GDC_sc uses a predefined “ characteristic atom ” near the end of each remainder for the evaluation of inter-residue distance deviations. An “ all atoms ” variant of the GDC score ( GDC_all ) is calculated using full-model information, and is one of the standard measures used by CASP ‘s organizers and assessors to evaluate accuracy of bode structural models. [ 5 ] [ 7 ] [ 11 ] GDT scores are broadly computed with esteem to a single reference structure. In some cases, geomorphologic models with lower GDT scores to a reference point structure determined by protein NMR are however full fits to the underlying experimental data. [ 12 ] Methods have been developed to estimate the uncertainty of GDT scores due to protein flexibility and doubt in the character structure. [ 13 ]
See besides [edit ]
- Root mean square deviation (bioinformatics) — A different structure comparison measure.
- TM-score — A different structure comparison measure.
References [edit ]
- CASP14 results – summary tables of the latest CASP experiment run in 2020, including example plots of GDT score as a function of cutoff distance
- GDT, GDC, LCS and LGA description services and documentation on structure comparison and similarity measures.