Int J Data Min Bioinform. 2008;2(2):145-56.

Large-scale Protein-Protein Interaction prediction using novel kernel methods.

Source

Electrical Engineering and Computer Science Department, The University of Kansas, Lawrence, KS 66045, USA. xwchen@ku.edu

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.

PMID:: 18767352; [PubMed - indexed for MEDLINE]

Publication Types, MeSH Terms, Substances, Grant Support

Publication Types

Research Support, N.I.H., Extramural

MeSH Terms

Substances

Proteome

Grant Support

P20 RR17708/RR/NCRR NIH HHS/United States

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