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PSSP-RFE: Accurate Prediction of Protein Structural Class by Recursive Feature Extraction from PSI-BLAST Profile, Physical-Chemical Property and Functional Annotations

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Listed:
  • Liqi Li
  • Xiang Cui
  • Sanjiu Yu
  • Yuan Zhang
  • Zhong Luo
  • Hua Yang
  • Yue Zhou
  • Xiaoqi Zheng

Abstract

Protein structure prediction is critical to functional annotation of the massively accumulated biological sequences, which prompts an imperative need for the development of high-throughput technologies. As a first and key step in protein structure prediction, protein structural class prediction becomes an increasingly challenging task. Amongst most homological-based approaches, the accuracies of protein structural class prediction are sufficiently high for high similarity datasets, but still far from being satisfactory for low similarity datasets, i.e., below 40% in pairwise sequence similarity. Therefore, we present a novel method for accurate and reliable protein structural class prediction for both high and low similarity datasets. This method is based on Support Vector Machine (SVM) in conjunction with integrated features from position-specific score matrix (PSSM), PROFEAT and Gene Ontology (GO). A feature selection approach, SVM-RFE, is also used to rank the integrated feature vectors through recursively removing the feature with the lowest ranking score. The definitive top features selected by SVM-RFE are input into the SVM engines to predict the structural class of a query protein. To validate our method, jackknife tests were applied to seven widely used benchmark datasets, reaching overall accuracies between 84.61% and 99.79%, which are significantly higher than those achieved by state-of-the-art tools. These results suggest that our method could serve as an accurate and cost-effective alternative to existing methods in protein structural classification, especially for low similarity datasets.

Suggested Citation

  • Liqi Li & Xiang Cui & Sanjiu Yu & Yuan Zhang & Zhong Luo & Hua Yang & Yue Zhou & Xiaoqi Zheng, 2014. "PSSP-RFE: Accurate Prediction of Protein Structural Class by Recursive Feature Extraction from PSI-BLAST Profile, Physical-Chemical Property and Functional Annotations," PLOS ONE, Public Library of Science, vol. 9(3), pages 1-10, March.
  • Handle: RePEc:plo:pone00:0092863
    DOI: 10.1371/journal.pone.0092863
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    References listed on IDEAS

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    1. Christopher Y Park & Aaron K Wong & Casey S Greene & Jessica Rowland & Yuanfang Guan & Lars A Bongo & Rebecca D Burdine & Olga G Troyanskaya, 2013. "Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes," PLOS Computational Biology, Public Library of Science, vol. 9(3), pages 1-14, March.
    2. Junfeng Gao & Zhao Wang & Yong Yang & Wenjia Zhang & Chunyi Tao & Jinan Guan & Nini Rao, 2013. "A Novel Approach for Lie Detection Based on F-Score and Extreme Learning Machine," PLOS ONE, Public Library of Science, vol. 8(6), pages 1-12, June.
    3. Xia-Yu Xia & Meng Ge & Zhi-Xin Wang & Xian-Ming Pan, 2012. "Accurate Prediction of Protein Structural Class," PLOS ONE, Public Library of Science, vol. 7(6), pages 1-8, June.
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