SOHSite: incorporating evolutionary information and physicochemical properties to identify protein S-sulfenylation sites

BMC Genomics
Van-Minh BuiTzong-Yi Lee

Abstract

Protein S-sulfenylation is a type of post-translational modification (PTM) involving the covalent binding of a hydroxyl group to the thiol of a cysteine amino acid. Recent evidence has shown the importance of S-sulfenylation in various biological processes, including transcriptional regulation, apoptosis and cytokine signaling. Determining the specific sites of S-sulfenylation is fundamental to understanding the structures and functions of S-sulfenylated proteins. However, the current lack of reliable tools often limits researchers to use expensive and time-consuming laboratory techniques for the identification of S-sulfenylation sites. Thus, we were motivated to develop a bioinformatics method for investigating S-sulfenylation sites based on amino acid compositions and physicochemical properties. In this work, physicochemical properties were utilized not only to identify S-sulfenylation sites from 1,096 experimentally verified S-sulfenylated proteins, but also to compare the effectiveness of prediction with other characteristics such as amino acid composition (AAC), amino acid pair composition (AAPC), solvent-accessible surface area (ASA), amino acid substitution matrix (BLOSUM62), position-specific scoring matrix (PSSM), and ...Continue Reading

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Citations

Dec 17, 2016·ACS Chemical Biology·Murugaeson R Kumar, Patrick J Farmer
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Methods Mentioned

BETA
X-Ray
features extraction
chemical modification

Software Mentioned

RVP
LIBSVM
BL2SEQ
- Net
SulfoSite
SOHSite
PSIPRED
WebLogo
InterPro
Net

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