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This allows us to train complex models of specificity without the risk of overfitting the training data.
Positively selected amino acid sites are shown to be located on either side of the active site cleft, an observation that is compatible with current models of specificity determination.
For example, classic cognitive theory identifies 'discounting the positives' as a common thinking error in depression (e.g. Beck, 1995) and the importance of examining positive content in models of specificity has been highlighted (Clark, Beck, & Alford, 1999).
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For this reason, more complex models of binding specificity have been developed.
In the current study, we generate custom data for human TFs in addition to using the yeast data from Gordân et al. (2013), and we focus on using feature selection to get more accurate and interpretable models of binding specificity.
For each model, estimates of specificity and positive and negative likelihood ratios (LR) were obtained given a baseline sensitivity of 85%, which has precedence in the literature as a reasonable cut-off level for biomarker comparison of Alzheimer's disease (AD) [38], [39].
The relationship between theory and model has been put in terms of the differential attitudes held by scientists (theories are believed while models are not); in terms of specificity (models as specifications of theories); and as the view that models are abstract entities that constitute theories.
These observations are consistent with a constrained model of PDZ specificity evolution where a set of initial PDZ domain specificities evolved, and that these were then expanded to form a finite number of subfamilies, each functionally similar down to the level of affinity determination.
A weakness of many ecological models is lack of specificity about which of the many acknowledged influences are most important [ 58].
The quantitative model of binding specificity of murine TAP developed herein should be useful for interpreting epitope mapping and immunogenicity data obtained in humanized mouse models.
This model of replicative specificity can likely be extended to other parvoviruses such as snake AAV which has a highly conserved T-shaped ITR structure but different spacer and nicking stem lengths [19].
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