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. 2016:2016:1654623.
doi: 10.1155/2016/1654623. Epub 2016 Jun 29.

Identification of Bacterial Cell Wall Lyases via Pseudo Amino Acid Composition

Xin-Xin Chen  1 , Hua Tang  2 , Wen-Chao Li  1 , Hao Wu  3 , Wei Chen  4 , Hui Ding  1 , Hao Lin  1
Affiliations

Identification of Bacterial Cell Wall Lyases via Pseudo Amino Acid Composition

Xin-Xin Chen et al. Biomed Res Int. 2016.

Abstract

Owing to the abuse of antibiotics, drug resistance of pathogenic bacteria becomes more and more serious. Therefore, it is interesting to develop a more reasonable way to solve this issue. Because they can destroy the bacterial cell structure and then kill the infectious bacterium, the bacterial cell wall lyases are suitable candidates of antibacteria sources. Thus, it is urgent to develop an accurate and efficient computational method to predict the lyases. Based on the consideration, in this paper, a set of objective and rigorous data was collected by searching through the Universal Protein Resource (the UniProt database), whereafter a feature selection technique based on the analysis of variance (ANOVA) was used to acquire optimal feature subset. Finally, the support vector machine (SVM) was used to perform prediction. The jackknife cross-validated results showed that the optimal average accuracy of 84.82% was achieved with the sensitivity of 76.47% and the specificity of 93.16%. For the convenience of other scholars, we built a free online server called Lypred. We believe that Lypred will become a practical tool for the research of cell wall lyases and development of antimicrobial agents.

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Figures

Figure 1
Figure 1
A heat map to show the overall accuracy in 5-fold cross-validation with different parameter groups (g, δ).
Figure 2
Figure 2
The ROC curve for the proposed model with the 63 optimal features in jackknife cross-validation using SVM.
Figure 3
Figure 3
A semiscreenshot to show the home page of Lypred. Its website address is http://lin.uestc.edu.cn/server/Lypred/.
See this image and copyright information in PMC

References

    1. Trudil D. Phage lytic enzymes: a history. Virologica Sinica. 2015;30(1):26–32. doi: 10.1007/s12250-014-3549-0. - DOI - PMC - PubMed
    1. Li Y., Wang C., Miao Z., et al. ViRBase: a resource for virus–host ncRNA-associated interactions. Nucleic Acids Research. 2015;43(1):D578–D582. doi: 10.1093/nar/gku903. - DOI - PMC - PubMed
    1. Hankin E. L'action bactericide des eaux de la Jumna et du Gange sur le vibrion du cholera. Annales de l'Institut Pasteur. 1896;10:511–523.
    1. Fischetti V. A. Bacteriophage lytic enzymes: novel anti-infectives. Trends in Microbiology. 2005;13(10):491–496. doi: 10.1016/j.tim.2005.08.007. - DOI - PubMed
    1. Osipovitch D. C., Therrien S., Griswold K. E. Discovery of novel S. aureus autolysins and molecular engineering to enhance bacteriolytic activity. Applied Microbiology and Biotechnology. 2015;99(15):6315–6326. doi: 10.1007/s00253-015-6443-2. - DOI - PMC - PubMed

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