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Journal of Biosciences

, Volume 40, Issue 4, pp 809–818 | Cite as

Protein–Protein interaction site prediction in Homo sapiens and E. coli using an interaction-affinity based membership function in fuzzy SVM

Article

Abstract

Protein–protein interaction (PPI) site prediction aids to ascertain the interface residues that participate in interaction processes. Fuzzy support vector machine (F-SVM) is proposed as an effective method to solve this problem, and we have shown that the performance of the classical SVM can be enhanced with the help of an interaction-affinity based fuzzy membership function. The performances of both SVM and F-SVM on the PPI databases of the Homo sapiens and E. coli organisms are evaluated and estimated the statistical significance of the developed method over classical SVM and other fuzzy membership-based SVM methods available in the literature. Our membership function uses the residue-level interaction affinity scores for each pair of positive and negative sequence fragments. The average AUC scores in the 10-fold cross-validation experiments are measured as 79.94% and 80.48% for the Homo sapiens and E. coli organisms respectively. On the independent test datasets, AUC scores are obtained as 76.59% and 80.17% respectively for the two organisms. In almost all cases, the developed F-SVM method improves the performances obtained by the corresponding classical SVM and the other classifiers, available in the literature.

Keywords

Fuzzy support vector machine interaction affinity protein–protein interaction 

Notes

Acknowledgements

This project is partially supported by the CMATER research laboratory of the Computer Science and Engineering Department, Jadavpur University, India, PURSE project and FASTTRACK grant (SR/FTP/ETA-04/2012) of DST, India.

Supplementary material

12038_2015_9564_MOESM1_ESM.pdf (423 kb)
ESM 1 (PDF 423 kb)

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Copyright information

© Indian Academy of Sciences 2015

Authors and Affiliations

  1. 1.Department of Computer Science and EngineeringGovernment College of Engineering and Leather TechnologyKolkataIndia
  2. 2.Department of Computer Science and EngineeringJadavpur UniversityKolkataIndia

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