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- Nazar Zaki
- College of Information Technology
- UAE University
I work in the College of Information Technology at UAE University.
Protein–protein interaction (PPI) is essential to most biological processes. Abnormal interactions may have implications in a number of neurological syndromes. We propose a simple yet effective method to detect PPI based on pairwise similarity and using only the primary structure of the protein. The PPI based on Pairwise Similarity (PPI-PS) method consists of a representation of each protein sequence by a vector of pairwise similarities against large subsequences of amino acids created by a shifting window which passes over concatenated protein training sequences. Each coordinate of this vector is typically the E-value of the Smith-Waterman score. These vectors are then used to compute the kernel matrix which will be exploited in conjunction with support vector machines. To assess the ability of the proposed method to recognize the difference between “interacted” and “non-interacted” proteins pairs, we applied it on different datasets from the available yeast saccharomyces cerevisiae protein interaction. The proposed method achieved reasonable improvement over the existing state-of-the-art methods for PPI prediction.
Experiment No. 1, 3 and 4 Download (Code, datasets) The file ReadMe_Ex1_3_4.doc contains the instructions to run the programs
Experiment No. 2 Download (Code, datasets) The file ReadMe_Ex2.doc contains the instructions to run the programs
Detailed Results: Download
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