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Generally scores below 0.20 corresponds to randomly chosen unrelated proteins whereas structures with a score higher than 0.5 assume roughly the same fold. [2] A quantitative study [3] shows that proteins of TM-score = 0.5 have a posterior probability of 37% in the same CATH topology family and of 13% in the same SCOP fold family. The ...
TM-align TM-score based protein structure alignment: Cα: Pair: nil: server and download: Y. Zhang & J. Skolnick: 2005 mTM-align Multiple protein structure alignment based on TM-align Cα Multi No server and download: R. Dong, Z. Peng, Y. Zhang & J. Yang 2018 VAST Vector Alignment Search Tool: SSE: Pair: nil: server: S. Bryant: 1996 PrISM
TM-score – a different structure comparison measure; Longest continuous segment (LCS) — A different structure comparison measure; Global distance calculation (GDC_sc, GDC_all) — Structure comparison measures that use full-model information (not just α-carbon) to assess similarity
Transitive Consistency Score (TCS) is an extended version of the T-Coffee scoring scheme. [14] It uses T-Coffee libraries of pairwise alignments to evaluate any third party MSA. Pairwise projections can be produced using fast or slow methods, thus allowing a trade-off between speed and accuracy.
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The rest of this article is focused on only multiple global alignments of homologous proteins. The first two are a natural consequence of most representations of alignments and their annotation being human-unreadable and best portrayed in the familiar sequence row and alignment column format, of which examples are widespread in the literature.
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 structure similarity assessment it is intended to use the GDT scores from several cutoff distances, and scores generally increase with increasing cutoff.
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