Prediction of protein–protein interactions with clustered amino acids and weighted sparse representation

Qiaoying Huang, Zhuhong You, Xiaofeng Zhang, Yong Zhou

Research output: Contribution to journalArticlepeer-review

28 Scopus citations

Abstract

With the completion of the Human Genome Project, bioscience has entered into the era of the genome and proteome. Therefore, protein–protein interactions (PPIs) research is becoming more and more important. Life activities and the protein–protein interactions are inseparable, such as DNA synthesis, gene transcription activation, protein translation, etc. Though many methods based on biological experiments and machine learning have been proposed, they all spent a long time to learn and obtained an imprecise accuracy. How to efficiently and accurately predict PPIs is still a big challenge. To take up such a challenge, we developed a new predictor by incorporating the reduced amino acid alphabet (RAAA) information into the general form of pseudo-amino acid composition (PseAAC) and with the weighted sparse representation-based classification (WSRC). The remarkable advantages of introducing the reduced amino acid alphabet is being able to avoid the notorious dimensionality disaster or overfitting problem in statistical prediction. Additionally, experiments have proven that our method achieved good performance in both a low- and high-dimensional feature space. Among all of the experiments performed on the PPIs data of Saccharomyces cerevisiae, the best one achieved 90.91% accuracy, 94.17% sensitivity, 87.22% precision and a 83.43% Matthews correlation coefficient (MCC) value. In order to evaluate the prediction ability of our method, extensive experiments are performed to compare with the state-of-the-art technique, support vector machine (SVM). The achieved results show that the proposed approach is very promising for predicting PPIs, and it can be a helpful supplement for PPIs prediction.

Original languageEnglish
Pages (from-to)10855-10869
Number of pages15
JournalInternational Journal of Molecular Sciences
Volume16
Issue number5
DOIs
StatePublished - 13 May 2015
Externally publishedYes

Keywords

  • Protein–protein interactions
  • Reduced amino acid alphabet
  • Weighted sparse representation-based classification

Fingerprint

Dive into the research topics of 'Prediction of protein–protein interactions with clustered amino acids and weighted sparse representation'. Together they form a unique fingerprint.

Cite this