protein attributes contribute to halo-stability, bioinformatics approach蛋白质属性有助于halo-stability,生物信息学的方法.pdfVIP

Ebrahimie et al. Saline Systems 2011, 7:1 /content/7/1/1 SALINE SYSTEMS RESEARCH Open Access Protein attributes contribute to halo-stability, bioinformatics approach 1 2* 1 3 Esmaeil Ebrahimie , Mansour Ebrahimi , Narjes Rahpayma Sarvestani and Mahdi Ebrahimi Abstract Halophile proteins can tolerate high salt concentrations. Understanding halophilicity features is the first step toward engineering halostable crops. To this end, we examined protein features contributing to the halo-toleration of halophilic organisms. We compared more than 850 features for halophilic and non-halophilic proteins with various screening, clustering, decision tree, and generalized rule induction models to search for patterns that code for halo-toleration. Up to 251 protein attributes selected by various attribute weighting algorithms as important features contribute to halo-stability; from them 14 attributes selected by 90% of models and the count of hydrogen gained the highest value (1.0) in 70% of attribute weighting models, showing the importance of this attribute in feature selection modeling. The other attributes mostly were the frequencies of di-peptides. No changes were found in the numbers of groups when K-Means and TwoStep clustering modeling were performed on datasets with or without feature selection filtering. Although the depths of induced trees were not high, the accuracies of trees were higher than 94% and the frequency of hydrophobic residues pointed as the most important feature to build trees. The performance evaluation of decision tree models had the same values and the best correctness percentage recorded with the Exhaust