Reduced amino acid alphabet is sufficient to accurately recognize intrinsically disordered protein - PubMed (original) (raw)

Reduced amino acid alphabet is sufficient to accurately recognize intrinsically disordered protein

Edward A Weathers et al. FEBS Lett. 2004.

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Abstract

Intrinsically disordered proteins are an important class of proteins with unique functions and properties. Here, we have applied a support vector machine (SVM) trained on naturally occurring disordered and ordered proteins to examine the contribution of various parameters (vectors) to recognizing proteins that contain disordered regions. We find that a SVM that incorporates only amino acid composition has a recognition accuracy of 87+/-2%. This result suggests that composition alone is sufficient to accurately recognize disorder. Interestingly, SVMs using reduced sets of amino acids based on chemical similarity preserve high recognition accuracy. A set as small as four retains an accuracy of 84+/-2%; this suggests that general physicochemical properties rather than specific amino acids are important factors contributing to protein disorder.

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