Short Communication: A method for discovering transmembrane beta-barrel proteins in Gram-negative bacterial proteomes

Authors:
Jing Hu;Changhui Yan
Affiliations:
Department of Computer Science, Utah State University, Logan, UT 84322, USA;Department of Computer Science, Utah State University, Logan, UT 84322, USA
Venue:
Computational Biology and Chemistry
Year:
2008

Citing 3
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Abstract

Transmembrane @b-barrel (TMB) proteins play pivotal roles in many aspects of bacterial functions. This paper presents a k-nearest neighbor (K-NN) method for discriminating TMB and non-TMB proteins. We start with a method that makes predictions based on a distance computed from residue composition and gradually improve the prediction performance by including homologous sequences and searching for a set of residues and di-peptides for calculating the distance. The final method achieves an accuracy of 97.1%, with 0.876 MCC, 86.4% sensitivity and 98.8% specificity. A web server based on the proposed method is available at http://yanbioinformatics.cs.usu.edu:8080/TMBKNNsubmit.