Measure of similarity between two protein structures
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.[1][2] 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.[1] 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.[1][3][4] The metric was first introduced as an evaluation standard in the third iteration of the biannual experiment (CASP3) in 1998.[3] 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).[5]
^ abcZemla A (2003). "LGA: A method for finding 3D similarities in protein structures". Nucleic Acids Research. 31 (13): 3370–3374. doi:10.1093/nar/gkg571. PMC 168977. PMID 12824330.
^US patent 8024127 B2, Adam Zemla, "Local-Global Alignment for Finding 3D Similarities in Protein Structures", issued 20 September 2011, assigned to Lawrence Livermore National Security, LLC
^ abZemla A, Venclovas C, Moult J, Fidelis K (1999). "Processing and analysis of CASP3 protein structure predictions". Proteins. S3 (S3): 22–29. doi:10.1002/(SICI)1097-0134(1999)37:3+<22::AID-PROT5>3.0.CO;2-W. PMID 10526349. S2CID 29803757.
^Zemla A, Venclovas C, Moult J, Fidelis K (2001). "Processing and evaluation of predictions in CASP4". Proteins. 45 (S5): 13–21. doi:10.1002/prot.10052. PMID 11835478. S2CID 28166260.
^Keedy, D.A.; Williams, CJ; Headd, JJ; Arendall, WB; Chen, VB; Kapral, GJ; Gillespie, RA; Block, JN; Zemla, A; Richardson, DC; Richardson, JS (2009). "The other 90% of the protein: Assessment beyond the α-carbon for CASP8 template-based and high-accuracy models". Proteins. 77 (Suppl 9): 29–49. doi:10.1002/prot.22551. PMC 2877634. PMID 19731372.
and 28 Related for: Global distance test information
The globaldistancetest (GDT), also written as GDT_TS to represent "total score", is a measure of similarity between two protein structures with known...
The Worldwide harmonized Light vehicles Test Procedure (WLTP) is a global driving cycle standard for determining the levels of pollutants, CO2 emission...
Geometric dimensioning and tolerancing, GD&T Global Descriptor Table, an x86 data structure Globaldistancetest, to compare proteins Ground Data Terminal...
results in the CASP14 edition of the competition, with a median globaldistancetest (GDT) score of 87.0 across protein targets in the challenging free-modeling...
Graham. "Global Express takes to the air." Flight International, 23 October 1996. "Global Expansion." Flight International, 3 July 1996. "Flight test on second...
produces P-value for relative global quality of a 3D model, GDT (GlobalDistanceTest) and uGDT (unnormalized-GDT) for absolute global quality of a 3D model and...
while RMSD and most other measures are length-dependent metrics. The GlobalDistanceTest (GDT) algorithm, and its GDT TS score to represent "total score"...
above 90% for around two-thirds of the proteins in CASP's globaldistancetest (GDT), a test that measures the degree of similarity between the structure...
zero all the way across), and is assigned a numerical score GDT-TS (GlobalDistanceTest—Total Score) describing percentage of well-modeled residues in the...
In common usage, climate change describes global warming—the ongoing increase in global average temperature—and its effects on Earth's climate system...
within distance ε of x∗ with x ≠ x∗, we have f(x∗) > f(x). Note that a point is a strict global maximum point if and only if it is the unique global maximum...
2006, Fossett flew the GlobalFlyer for the longest aircraft flight distance in history: 25,766 miles (41,466 km). The GlobalFlyer was specifically designed...
learning algorithms since each test sample's predicted result requires a fully computed distance matrix between the test sample and each training sample...
Distance education, also known as distance learning, is the education of students who may not always be physically present at school, or where the learner...
more sophisticated measures of structural similarity such as the globaldistancetest (GDT, the metric used in CASP). The structural alignment also implies...
mathematics and its applications, the signed distance function (or oriented distance function) is the orthogonal distance of a given point x to the boundary of...
The Presidential Fitness Test was a national physical fitness testing program conducted in United States public middle and high schools from the late 1950s...
The Rorschach test is a projective psychological test in which subjects' perceptions of inkblots are recorded and then analyzed using psychological interpretation...
camera, the flange focal distance (FFD) (also known as the flange-to-film distance, flange focal depth, flange back distance (FBD), flange focal length...
navigation aid developed by the Federal Aviation Administration to augment the Global Positioning System (GPS), with the goal of improving its accuracy, integrity...
multisport race consisting of swimming, cycling, and running over various distances. Triathletes compete for fastest overall completion time, racing each...
slope indicate the global (macro) structure, clusters and switches evaluate the performance’s local (micro) structure. Verbal fluency tests have been validated...
The Global Positioning System (GPS), originally Navstar GPS, is a satellite-based radio navigation system owned by the United States government and operated...
consumption of urban and extra-urban cycles over the total distance (theoretical 10932 meters). The total test time amounts to 1180 s with an average speed of 33...
2018. "Global growth | Cambridge Assessment". www.cambridgeassessment.org.uk. Retrieved 30 June 2020. "Cambridge buys into Box Hill English test". www...
One participant in the test saw a bright flash through dark goggles and felt the effects of a thermal pulse even at a distance of 270 km (170 mi). The...
a global survey of the values of IBM employees conducted from 1967 and 1973. Hofstede's theory identified six dimensions of culture: power distance, individualism...
Global Information