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In Homology Modeling, each alignment is given a likelihood score. This score attempts to calculate the probability that a particular template/alignment is among the top 2% GDT (Global Distance Test, Zemla et al., Proteins, 1999) score for a particular target. The likelihood measure only considers two factors when assigning a value: the generation method, and the method’s ranking of the alignment. The values used were determined by evaluating the performance of each alignment method on a large benchmark set of 1,431 targets (Song et al., Structure, 2013); a function of the following form was fit to this data:

Here, mthd is the alignment method used, and rank is the individual method’s ranking of the alignment.