Article

Predict mycobacterial proteins subcellular locations by incorporating pseudo-average chemical shift into the general form of Chou's pseudo amino acid composition

Department of Physics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.
Journal of Theoretical Biology (Impact Factor: 2.12). 03/2012; 304:88-95. DOI: 10.1016/j.jtbi.2012.03.017
Source: PubMed

ABSTRACT

Mycobacterium tuberculosis (MTB) is a pathogenic bacterial species in the genus Mycobacterium and the causative agent of most cases of tuberculosis (Berman et al., 2000). Knowledge of the localization of Mycobacterial protein may help unravel the normal function of this protein. Automated prediction of Mycobacterial protein subcellular localization is an important tool for genome annotation and drug discovery. In this work, a benchmark data set with 638 non-redundant mycobacterial proteins is constructed and an approach for predicting Mycobacterium subcellular localization is proposed by combining amino acid composition, dipeptide composition, reduced physicochemical property, evolutionary information, pseudo-average chemical shift. The overall prediction accuracy is 87.77% for Mycobacterial subcellular localizations and 85.03% for three membrane protein types in Integral membranes using the algorithm of increment of diversity combined with support vector machine. The performance of pseudo-average chemical shift is excellent. In order to check the performance of our method, the data set constructed by Rashid was also predicted and the accuracy of 98.12% was obtained. This indicates that our approach was better than other existing methods in literature.

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    • "The online web server PSIPRED (http://bioinf.cs.ucl.ac.uk/psipred/) was used to obtain the predicted secondary structure of each protein sequence in the 76-protein fold class dataset. We calculated the ACS using a previously described method (Mielke and Krishnan, 2003; Fan and Li, 2012a; Fan and Li, 2012b; Fan et al., 2013; Fan and Li, 2013; Anaika et al., 2003). We selected chemical shift values of 1 H a and 1 H N (two types of protein backbone atoms for every amino acid residue of protein sequence P) to calculate the corresponding ACS. "
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    • "More information for prediction of subcellular localization was shown in two comprehensive review papers (Chou and Shen, 2007; Nakai, 2000). Moreover, many new algorithms were established for identifying the subcellular localization in recent years (Chou and Shen, 2010a, 2010b; Chou et al., 2011, 2012; Fan and Li, 2012; Mei, 2012; Wan et al., 2013; Wu et al., 2011, 2012; Xiao et al., 2011a, 2011b). Although various experimental techniques and computational approaches have been developed and used to identify subcellular localizations of proteins (Chou and Shen, 2007; Dreger, 2003; Gygi et al., 1999; Nakai, 2000; Tsien, 1998), however, to date, only a few attempts have been made to globally analyze proteins in different subcellular localizations (Drawid et al., 2000; Ghaemmaghami et al., 2003; Martin and MacNeill, 2004; Wang et al., 2013). "
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