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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.
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
The score combines the log-likelihood of the alignment, a covariation term and the basepair probabilities. any: Yes: Yes: No: sourcecode [67] [68] Multilign: This method uses multiple Dynalign calculations to find a low free energy structure common to any number of sequences. It does not require any sequence identity. any: Yes: Yes: No ...
Tree calculation tool calculates phylogenetic tree using BioJava API and lets user draw trees using Archaeopteryx: Software is package of 7 interactive visual tools for multiple sequence alignments. Major focus is manipulating large alignments. Includes MSApad, MSA comparator, MSA reconstruction tool, FASTA generator and MSA ID matrix calculator
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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In statistics, the 68–95–99.7 rule, also known as the empirical rule, and sometimes abbreviated 3sr, is a shorthand used to remember the percentage of values that lie within an interval estimate in a normal distribution: approximately 68%, 95%, and 99.7% of the values lie within one, two, and three standard deviations of the mean, respectively.
Calculate a similarity score that is the sum of the joined regions penalising for each gap 20 points. This initial similarity score (initn) is used to rank the library sequences. The score of the single best initial region found in step 2 is reported (init1).