Validating accuracy of web server statistics
Application of this methodology to the prion protein showed that conformationally variable positions predicted in its ordered C-terminal domain are located within segments presumed to be involved in refolding of Pr P.
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The highest prediction accuracy is achieved using a classifier that utilizes a combination of evolutionary conservation and low-resolution structural information (Figure 5). ROC curves of the SVM predictors of DNA-binding sites.
The predictors have the following values of the area under the curve (AUC): seq-SVM AUC=0.748; seq-str-SVM AUC=0.776; pssm-SVM AUC=0.836; pssm-str-SVM AUC=0.840.
Broadly, protein flexibility can be classified into two overlapping categories: (1) disordered flexibility observed in intrinsically-unstructured segments that do not have a well-defined folded structure and (2) ordered flexibility observed in segments that adopt at least two different folded conformations. Japanese encephalitis virus envelope protein E: a model of conformational transition upon membrane fusion.
A moving loop on the left side represents an artifact resulting from an unstructured fragment missing electron density. We developed Generalized Local Propensity (GLP) profile, a novel quantitative sequence-based measure of conformational flexibility in proteins and showed that GLP is able to discriminate between different types of conformational flexibility (Kuznetsov and Rackovsky, 2003a).