Global distance test
Encyclopedia
The global distance test or GDT (also written as GDT_TS to represent "total score") is a measure of similarity between two protein structure
s with identical amino acid sequences but different tertiary structure
s. It is most commonly used to compare the results of protein structure prediction
to the experimentally determined structure as measured by X-ray crystallography
or protein NMR. The metric is intended as a more accurate measurement than the more common RMSD metric, which is sensitive to outlier
regions created by poor modeling of individual loop regions in a structure that is otherwise reasonably accurate. 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 and identifying their primary deficiencies.
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. It is typical to calculate the GDT score under several cutoff distances, and scores generally increase with increasing cutoff. A plateau in this increase may indicate an extreme divergence between the experimental and predicted structures, such that no additional atoms are included in any cutoff of a reasonable distance.
The high accuracy version of the GDT measure is called GDT-HA. It uses smaller cut off distances (half the size of GDT_TS) and thus is more rigorous.
Protein structure
Proteins are an important class of biological macromolecules present in all organisms. Proteins are polymers of amino acids. Classified by their physical size, proteins are nanoparticles . Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20 possible L-α-amino...
s with identical amino acid sequences but different tertiary structure
Tertiary structure
In biochemistry and molecular biology, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.-Relationship to primary structure:...
s. It is most commonly used to compare the results of protein structure prediction
Protein structure prediction
Protein structure prediction is the prediction of the three-dimensional structure of a protein from its amino acid sequence — that is, the prediction of its secondary, tertiary, and quaternary structure from its primary structure. Structure prediction is fundamentally different from the inverse...
to the experimentally determined structure as measured by X-ray crystallography
X-ray crystallography
X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a...
or protein NMR. The metric is intended as a more accurate measurement than the more common RMSD metric, which is sensitive to outlier
Outlier
In statistics, an outlier is an observation that is numerically distant from the rest of the data. Grubbs defined an outlier as: An outlying observation, or outlier, is one that appears to deviate markedly from other members of the sample in which it occurs....
regions created by poor modeling of individual loop regions in a structure that is otherwise reasonably accurate. GDT_TS measurements are used as major assessment criteria in the production of results from the Critical Assessment of Structure Prediction
CASP
CASP, which stands for Critical Assessment of Techniques for Protein Structure Prediction, is a community-wide, worldwide experiment for protein structure prediction taking place every two years since 1994...
(CASP), a large-scale experiment in the structure prediction community dedicated to assessing current modeling techniques and identifying their primary deficiencies.
The GDT score is calculated as the largest set of amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
residues' alpha carbon
Alpha carbon
The alpha carbon in organic chemistry refers to the first carbon that attaches to a functional group . By extension, the second carbon is the beta carbon, and so on....
atoms in the model structure falling within a defined distance cutoff of their position in the experimental structure. It is typical to calculate the GDT score under several cutoff distances, and scores generally increase with increasing cutoff. A plateau in this increase may indicate an extreme divergence between the experimental and predicted structures, such that no additional atoms are included in any cutoff of a reasonable distance.
The high accuracy version of the GDT measure is called GDT-HA. It uses smaller cut off distances (half the size of GDT_TS) and thus is more rigorous.
See also
- RMSD — A different structure comparison measure
- TM-ScoreTemplate Modeling Score (bioinformatics)The Template Modeling Score or TM-score is a measure of similarity between two protein structures with different tertiary structures. The TM-score is intended as a more accurate measure of the quality of full-length protein structures than the often used RMSD and GDT measures...
— A different structure comparison measure - LCS — A different structure comparison measure
External links
- CASP6 results plotted by GDT score for each target structure included in the experiment