TMB-Hunt: An amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins

Background: Beta-barrel transmembrane (bbtm) proteins are a functionally important and diverse group of proteins expressed in the outer membranes of bacteria (both gram negative and acid fast gram positive), mitochondria and chloroplasts. Despite recent publications describing reasonable levels of accuracy for discriminating between bbtm proteins and other proteins, screening of entire genomes remains troublesome as these molecules only constitute a small fraction of the sequences screened. Therefore, novel methods are still required capable of detecting new families of bbtm protein in diverse genomes. Results: We present TMB-Hunt, a program that uses a k-Nearest Neighbour (k-NN) algorithm to discriminate between bbtm and non-bbtm proteins on the basis of their amino acid composition. By including differentially weighted amino acids, evolutionary information and by calibrating the scoring, an accuracy of 92.5% was achieved, with 91% sensitivity and 93.8% positive predictive value (PPV...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Andrew G. Garrow, Alison Agnew, David R. Westhead
• Keywords: Amino Acids, Bbtm Protein, BMCBI 2005, Proteins