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Amino Acids. 2008 Jun;35(1):65-73. doi: 10.1007/s00726-007-0628-7. Epub 2008 Jan 25.

Discrimination of outer membrane proteins using a K-nearest neighbor method.

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Department of Computer Science, Utah State University, Logan, UT 84322-4205, USA.


Identification of outer membrane proteins (OMPs) from genome is an important task. This paper presents a k-nearest neighbor (K-NN) method for discriminating outer membrane proteins (OMPs). The method makes predictions based on a weighted Euclidean distance that is computed from residue composition. The method achieves 89.1% accuracy with 0.668 MCC (Matthews correlation coefficient) in discriminating OMPs and non-OMPs. The performance of the method is improved by including homologous information into the calculation of residue composition. The final method achieves an accuracy of 96.1%, with 0.873 MCC, 87.5% sensitivity, and 98.2% specificity. Comparisons with multiple recently published methods show that the method proposed in this study outperforms the others.

[Indexed for MEDLINE]

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