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Predicting Caspase Substrate Cleavage Sites Based on a Hybrid SVMPSSM Method

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Caspases play an important role in many critical non-apoptosis processes by cleaving relevant substrates at cleavage sites. Identification of caspase substrate cleavage sites is the key to understand these processes. This paper proposes a hybrid method using support vector machine (SVM) in conjunction with position specific scoring matrices (PSSM) for caspase substrate cleavage sites prediction. Three encoding schemes including orthonormal binary encoding, BLOSUM62 matrix profile and PSSM profile of neighborhood surrounding the substrate cleavage sites were regarded as the input of SVM. The 10-fold cross validation results demonstrate that the SVM-PSSM method performs well with an overall accuracy of 97.619% on a larger dataset.

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Keywords: B-cell epitope; BLOSUM62 matrix; BLOSUM62 matrix profile; CASBAH database; CAspase; Caspase; GalNAc-transferase; HIV protease; Hybrid SVMPSSM Method; MEROPS protease database; Matthews's Correlation Coefficient; P4-P3-P2-P1; PSSM profiles; Position Specific Score Matrix; SVM; SVM-PSSM method; Substrate dataBAse; alanine; alpha-turn types; benchmark dataset; caspase 3; cathepsin B; crossvalidation; cysteine proteases; granzyme B; jackknife test; mammalian cell death; orthonormal binary encoding; radial basis function; serine hydrolases; substrate cleavage sites prediction; support vector machine; valine

Document Type: Research Article

Publication date: 2010-12-01

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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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