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Studies on biochemical properties, gene configuration, active-site chemical models and site-directed mutagenesis have given the insight into the structural and functional characteristics of NHase.
Simulations incorporating the attenuation models and site correction improved the prediction of the S-wave envelope, duration, and peak ground acceleration (PGA).
This result further supports the estimates obtained at the codon level by applying Paralog models and site-models to separate datasets of the paralogs (see previous section).
By selectivity of a PWM model we refer to the ability of the model to distinguish between sites generated by the model and "sites" observed in "random DNA".
The positively selected sites found by site models and branch-site models were located on the SMase D three-dimensional structure (see below).
Table 3 lists the log likelihood values and parameter estimates for the C-terminal domain of PCSK9 under several site models and branch-site models.
We applied the different codon substitution models implemented in codeml (Branch Models, Site Models and Branch-Site Models).
Three approaches were employed: branch models, site models and branch-site models with the use of the PAML package.
We used both site models and branch-site models to detect positive selection.
According to different studies [ 19– 24, 34], our first approach to address this problem consisted in the analysis of branch models, site models, and branch-site models.
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