Journal
AMINO ACIDS
Volume 43, Issue 2, Pages 545-555Publisher
SPRINGER WIEN
DOI: 10.1007/s00726-011-1143-4
Keywords
Submitochondria location; Increment of diversity; Average chemical shift; Support vector machine; Chou's pseudo amino acid
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Funding
- National Natural Science Foundation of China [61063016, 31160188]
- Research Fund for the Doctoral Program of Higher Education of China [20101501110004]
- Inner Mongolia University [2-1.2.1_035, 208152]
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Knowledge of the submitochondria location of protein is integral to understanding its function and a necessity in the proteomics era. In this work, a new submitochondria data set is constructed, and an approach for predicting protein submitochondria locations is proposed by combining the amino acid composition, dipeptide composition, reduced physicochemical properties, gene ontology, evolutionary information, and pseudo-average chemical shift. The overall prediction accuracy is 93.57% for the submitochondria location and 97.79% for the three membrane protein types in the mitochondria inner membrane using the algorithm of the increment of diversity combined with the support vector machine. The performance of the pseudo-average chemical shift is excellent. For contrast, the method is also used to predict submitochondria locations in the data set constructed by Du and Li; an accuracy of 94.95% is obtained by our method, which is better than that of other existing methods.
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