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  • Title: Large-scale Protein-Protein Interaction prediction using novel kernel methods.
    Author: Chen XW, Han B, Fang J, Haasl RJ.
    Journal: Int J Data Min Bioinform; 2008; 2(2):145-56. PubMed ID: 18767352.
    Abstract:
    Knowledge of Protein-Protein Interactions (PPIs) can give us new insights into molecular mechanisms and properties of the cell. In this paper, we propose a novel domain-based kernel method to predict PPIs. A new kernel that measures the similarity between protein pairs based on a new feature representation is developed and applied to a large scale PPI database. Experimental results demonstrate its effectiveness. Furthermore, we evaluate the problem of cross-species PPI prediction and the effect of the number of negative samples on the performance of PPI predictions, which are two fundamental problems in most in silico PPI methods.
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