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Predicting the types of J-proteins using clustered amino acids.

Pengmian FengHao LinWei ChenYongchun Zuo
Published in: BioMed research international (2014)
J-proteins are molecular chaperones and present in a wide variety of organisms from prokaryote to eukaryote. Based on their domain organizations, J-proteins can be classified into 4 types, that is, Type I, Type II, Type III, and Type IV. Different types of J-proteins play distinct roles in influencing cancer properties and cell death. Thus, reliably annotating the types of J-proteins is essential to better understand their molecular functions. In the present work, a support vector machine based method was developed to identify the types of J-proteins using the tripeptide composition of reduced amino acid alphabet. In the jackknife cross-validation, the maximum overall accuracy of 94% was achieved on a stringent benchmark dataset. We also analyzed the amino acid compositions by using analysis of variance and found the distinct distributions of amino acids in each family of the J-proteins. To enhance the value of the practical applications of the proposed model, an online web server was developed and can be freely accessed.
Keyphrases
  • amino acid
  • cell death
  • squamous cell carcinoma
  • machine learning
  • single molecule
  • young adults
  • small molecule
  • gram negative
  • squamous cell
  • protein protein