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. 2014;2014:947416.
doi: 10.1155/2014/947416. Epub 2014 May 22.

iMethyl-PseAAC: Identification of Protein Methylation Sites via a Pseudo Amino Acid Composition Approach

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Free PMC article

iMethyl-PseAAC: Identification of Protein Methylation Sites via a Pseudo Amino Acid Composition Approach

Wang-Ren Qiu et al. Biomed Res Int. .
Free PMC article

Abstract

Before becoming the native proteins during the biosynthesis, their polypeptide chains created by ribosome's translating mRNA will undergo a series of "product-forming" steps, such as cutting, folding, and posttranslational modification (PTM). Knowledge of PTMs in proteins is crucial for dynamic proteome analysis of various human diseases and epigenetic inheritance. One of the most important PTMs is the Arg- or Lys-methylation that occurs on arginine or lysine, respectively. Given a protein, which site of its Arg (or Lys) can be methylated, and which site cannot? This is the first important problem for understanding the methylation mechanism and drug development in depth. With the avalanche of protein sequences generated in the postgenomic age, its urgency has become self-evident. To address this problem, we proposed a new predictor, called iMethyl-PseAAC. In the prediction system, a peptide sample was formulated by a 346-dimensional vector, formed by incorporating its physicochemical, sequence evolution, biochemical, and structural disorder information into the general form of pseudo amino acid composition. It was observed by the rigorous jackknife test and independent dataset test that iMethyl-PseAAC was superior to any of the existing predictors in this area.

Figures

Figure 1
Figure 1
Schematic drawing to show the involvement of the Arg-methylation and Lys-methylation in gene regulation (adapted from [13] with permission).
Figure 2
Figure 2
Schematic drawing to show the Chou's peptide formulation for studying (a) Arg-methylation and (b) Lys-methylation (adapted from [32, 33] with permission).
Figure 3
Figure 3
A semiscreenshot to show the top page of iMethyl-PseAAC. Its web-site address is at http://www.jci-bioinfo.cn/iMethyl-PseAAC.

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