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Mathematical Problems in Engineering
Volume 2015, Article ID 857325, 9 pages
Research Article

Prediction of “Aggregation-Prone” Peptides with Hybrid Classification Approach

1School of Physical Education, Northeast Normal University, Changchun 130117, China
2School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China

Received 23 July 2014; Revised 29 September 2014; Accepted 29 September 2014

Academic Editor: Shifei Ding

Copyright © 2015 Bo Liu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Protein aggregation is a biological phenomenon caused by misfolding proteins aggregation and is associated with a wide variety of diseases, such as Alzheimer’s, Parkinson’s, and prion diseases. Many studies indicate that protein aggregation is mediated by short “aggregation-prone” peptide segments. Thus, the prediction of aggregation-prone sites plays a crucial role in the research of drug targets. Compared with the labor-intensive and time-consuming experiment approaches, the computational prediction of aggregation-prone sites is much desirable due to their convenience and high efficiency. In this study, we introduce two computational approaches Aggre_Easy and Aggre_Balance for predicting aggregation residues from the sequence information; here, the protein samples are represented by the composition of k-spaced amino acid pairs (CKSAAP). And we use the hybrid classification approach to predict aggregation-prone residues, which integrates the naïve Bayes classification to reduce the number of features, and two undersampling approaches EasyEnsemble and BalanceCascade to deal with samples imbalance problem. The Aggre_Easy achieves a promising performance with a sensitivity of 79.47%, a specificity of 80.70% and a MCC of 0.42; the sensitivity, specificity, and MCC of Aggre_Balance reach 70.32%, 80.70% and 0.42. Experimental results show that the performance of Aggre_Easy and Aggre_Balance predictor is better than several other state-of-the-art predictors. A user-friendly web server is built for prediction of aggregation-prone which is freely accessible to public at the website.