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April 22, 2015:
MDD-SOH : a web server was constructed for identifying S-Sulfenylation sites.

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Version: 1.0
(April 22, 2015)


Welcome to MDD-SOH!

MDD-SOH is a web server for identifying S-sulfenylation sites. Cysteine S-sulfenylation (S-sulphenylation or sulfenic acid), involving the covalent attachment of S-hydroxylation (-SOH) to cysteine thiol, plays an important role in redox regulation of protein functions. Although the characteristic of sulfenic acid is transient and labile, most of physiological activities have occurred under control of S-hydroxylation. Therefore, discriminating the specific site of S-sulfenylation proteins are essential tasks in computational biology for the furtherance of structural and functional protein. Until now, the research in S-sulfenylation protein is still limited. In addition, there are no any tools to help to find the sulfenylation sites.

In this study, based on a total of 901 S-sulfenylation proteins, our studies carry out an informatics investigation on S-sulfenylation sites based on structural factors: the flanking amino acids composition and the solvent-accessible surface are (ASA). Utilizing the TwoSampleLogo, the positively charged amino acids flanking the S-sulfenylated cysteine may impact the formulation of S-sulfenylation in closed three dimensional environments. Our study also investigates some features and then, two or more ones are incorporated to generate the best model. Being founded on the advantage of Support Vector Machine (SVM), this approach is applied to build the predicted model for identifying Sulfenic-sites. In order to overcome the difficulties in finding the conserved motifs, the maximal dependence decomposition (MDD) is applicable to solve the problem. Following our five-fold cross validation results, as MDD-clustered models are applied, it leads to significant positive changes in all measurement units: sensitivity, specificity, accuracy and MCC. Moreover, it also efficaciously enhances the performance in an independent test set.

The constructed models are chosen to implement an effective web-based tool, named MDD-SOH (http://csb.cse.yzu.edu.tw/MDDSOH/), for identifying uncharacterized S-sulfenylation sites on the protein sequences.

  • Case Study 1 : FABP5_HUMAN, Fatty acid-binding protein, epidermal.
  • Case Study 2 : PRDX6_HUMAN, Peroxiredoxin-6.
  • Case Study 3 : GPX3_YEAST, Peroxiredoxin HYR1.
  • Investigation of S-sulfenylation sites

    Protein sulfenic acid (also known as S-sulfenylation or S-sulphenylation, abbreviated as Cys-SOH) is a reversible post-translation modification (PTM) involving the covalent attachment of hydrogen oxide to the thiol group of cysteine residues, adding 16 Da to the modified proteins. Over the last decade, oxidation of the thiol functional group in cysteine (Cys–SH) to sulfenic (Cys–SOH) is emerging as an outstanding post-translational modification that plays an influential role in controlling state of proteins function under both physiologic and oxidative stress conditions. To get a better understanding and characterize the potential linear consensus motif and adjacent amino acids surrounding to sulfenylated cysteine residues, 1,031 S-sulfenylated cysteines are further compared with the free cysteines by two sample logo.




    Submission


  • Case Study 1 : FABP5_HUMAN, Fatty acid-binding protein, epidermal.
  • Case Study 2 : PRDX6_HUMAN, Peroxiredoxin-6.
  • Case Study 3 : GPX3_YEAST, Peroxiredoxin HYR1.