jEcho: an Evolved weight vector to CHaracterize the protein's posttranslational modification mOtifs.

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jEcho: an Evolved weight vector to CHaracterize the protein’s posttranslational modification mOtifs.

Interdiscip Sci. 2015 Jun;7(2):194-9

Authors: Zhao M, Zhang Z, Mai G, Luo Y, Zhou F

Protein’s posttranslational modification (PTM) represents a major dynamic regulation of protein functions after the translation of polypeptide chains from mRNA molecule. Compared with the costly and labor-intensive wet laboratory characterization of PTMs, the computer-based detection of PTM residues has been a major complementary technique in recent years. Previous studies demonstrated that the PTM-flanking positions convey different contributions to the computational detection of PTM residue, but did not directly translate this observation into the in silico PTM prediction. We propose a weight vector to represent the variant contributions of the PTM-flanking positions and use an evolutionary algorithm to optimize the vector. Even a simple nearest neighbor algorithm with the incorporated optimal weight vector outperforms the currently available algorithms. The algorithm is implemented as an easy-to-use computer program, jEcho version 1.0. The implementation language, Java, makes jEcho platform-independent and visually interactive. The predicted results may be directly exported as publication-quality images or text files. jEcho may be downloaded from .

PMID: 26245277 [PubMed – indexed for MEDLINE]

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