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FEBS Lett. 2004 Oct 22;576(3):348-52.

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

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Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 221 Maryland Hall, 3400 North Charles Street, Baltimore, MD 21218, USA.


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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