The global distance test (GDT), also written as GDT_TS to represent "total score", is a measure of similarity between two protein structures with known amino acid correspondences (e.g. identical amino acid sequences) but different tertiary structures. It is most commonly used to compare the results of protein structure prediction to the experimentally determined structure as measured by X-ray crystallography, protein NMR, or, increasingly, cryoelectron microscopy. The metric was developed by Adam Zemla at Lawrence Livermore National Laboratory and originally implemented in the Local-Global Alignment (LGA) program. It is intended as a more accurate measurement than the common root-mean-square deviation (RMSD) metric - which is sensitive to outlier regions created, for example, by poor model
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| - Global distance test (en)
- グローバル距離テスト (ja)
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| - グローバル距離テスト (global distance test、GDT) は、既知のアミノ酸対応を持ちながら (例えば同一のアミノ酸配列)、三次構造が異なる2つのタンパク質構造間の類似性を測定する尺度であり、「合計スコア」を表すためにGDT_TSとも呼ばれる。これは、タンパク質の構造予測の結果を、X線結晶構造解析またはによって測定された実験的に決定された構造と比較するために最も一般的に使用される。著者のAdam Zemla氏が説明するGDT測定値は、より一般的なRMSD測定値よりも正確な測定を目的としており、これは構造中の個々のループ領域のモデル化が不十分なために外れ値領域の影響を受けやすいが、それ以外の場合は適度に正確である。GDT_TS測定値は、タンパク質構造予測精密評価 (CASP、Critical Assessment of Structure Prediction) の結果を作成する際の主要な評価基準として使用される。CASPは、現在のモデリング技術の評価と、その主要な欠陥を特定に特化した構造予測コミュニティでの大規模な実験である。一般的にGDT_TSが高いほど、参照構造と比較して与えられたモデルが優れている。 (ja)
- The global distance test (GDT), also written as GDT_TS to represent "total score", is a measure of similarity between two protein structures with known amino acid correspondences (e.g. identical amino acid sequences) but different tertiary structures. It is most commonly used to compare the results of protein structure prediction to the experimentally determined structure as measured by X-ray crystallography, protein NMR, or, increasingly, cryoelectron microscopy. The metric was developed by Adam Zemla at Lawrence Livermore National Laboratory and originally implemented in the Local-Global Alignment (LGA) program. It is intended as a more accurate measurement than the common root-mean-square deviation (RMSD) metric - which is sensitive to outlier regions created, for example, by poor model (en)
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| - The global distance test (GDT), also written as GDT_TS to represent "total score", is a measure of similarity between two protein structures with known amino acid correspondences (e.g. identical amino acid sequences) but different tertiary structures. It is most commonly used to compare the results of protein structure prediction to the experimentally determined structure as measured by X-ray crystallography, protein NMR, or, increasingly, cryoelectron microscopy. The metric was developed by Adam Zemla at Lawrence Livermore National Laboratory and originally implemented in the Local-Global Alignment (LGA) program. It is intended as a more accurate measurement than the common root-mean-square deviation (RMSD) metric - which is sensitive to outlier regions created, for example, by poor modeling of individual loop regions in a structure that is otherwise reasonably accurate. The conventional GDT_TS score 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 score, the more closely a model approximates a given reference structure. GDT_TS measurements are used as major assessment 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 modeling techniques. The metric was first introduced as an evaluation standard in the third iteration of the biannual experiment (CASP3) in 1998. Various extensions to the original method have been developed; variations that accounts for the positions of the side chains are known as global distance calculations (GDC). (en)
- グローバル距離テスト (global distance test、GDT) は、既知のアミノ酸対応を持ちながら (例えば同一のアミノ酸配列)、三次構造が異なる2つのタンパク質構造間の類似性を測定する尺度であり、「合計スコア」を表すためにGDT_TSとも呼ばれる。これは、タンパク質の構造予測の結果を、X線結晶構造解析またはによって測定された実験的に決定された構造と比較するために最も一般的に使用される。著者のAdam Zemla氏が説明するGDT測定値は、より一般的なRMSD測定値よりも正確な測定を目的としており、これは構造中の個々のループ領域のモデル化が不十分なために外れ値領域の影響を受けやすいが、それ以外の場合は適度に正確である。GDT_TS測定値は、タンパク質構造予測精密評価 (CASP、Critical Assessment of Structure Prediction) の結果を作成する際の主要な評価基準として使用される。CASPは、現在のモデリング技術の評価と、その主要な欠陥を特定に特化した構造予測コミュニティでの大規模な実験である。一般的にGDT_TSが高いほど、参照構造と比較して与えられたモデルが優れている。 (ja)
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