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A method for discovering transmembrane beta-barrel proteins in Gram-negative bacterial proteomes. (English) Zbl 1158.92015

Summary: Transmembrane \(\beta \)-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 compositions and gradually improves 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.

MSC:

92C40 Biochemistry, molecular biology
62P10 Applications of statistics to biology and medical sciences; meta analysis
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