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Prediction of Protein Secondary Structure Content by Using the Concept of Chou's Pseudo Amino Acid Composition and Support Vector Machine

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Protein secondary structure carries information about local structural arrangements. Significant majority of successful methods for predicting the secondary structure is based on multiple sequence alignment. However, the multiple alignment fails to achieve accurate results when a protein sequence is characterized by low homology. To this end, we propose a novel method for prediction of secondary structure content through comprehensive sequence representation. The method is featured by employing a support vector machine (SVM) regressing system and adopting a different pseudo amino acid composition (PseAAC), which can partially take into account the sequence-order effects to represent protein samples. It was shown by both the self-consistency test and the independent-dataset test that the trained SVM has remarkable power in grasping the relationship between the PseAAC and the content of protein secondary structural elements, including α-helix, 310-helix, π-helix, β-strand, β-bridge, turn, bend and the rest random coil. Results prior to or competitive with the popular methods have been obtained, which indicate that the present method may at least serve as an alternative to the existing predictors in this area.

Keywords: Pseudo Amino acid composition; prediction; protein secondary structure content; support vector machine

Document Type: Research Article


Publication date: 2009-01-01

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  • Protein & Peptide Letters publishes short papers in all important aspects of protein and peptide research, including structural studies, recombinant expression, function, synthesis, enzymology, immunology, molecular modeling, drug design etc. Manuscripts must have a significant element of novelty, timeliness and urgency that merit rapid publication. Reports of crystallisation, and preliminary structure determinations of biologically important proteins are acceptable. Purely theoretical papers are also acceptable provided they provide new insight into the principles of protein/peptide structure and function.
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