Improving the detection of transmembrane β-barrel chains with N-to-1 extreme learning machines

Abstract Motivation: Transmembrane β-barrels (TMBBs) are extremely important proteins that play key roles in several cell functions. They cross the lipid bilayer with β-barrel structures. TMBBs are presently found in the outer membranes of Gram-negative bacteria and of mitochondria and chloroplasts. Loop exposure outside the bacterial cell membranes makes TMBBs important targets for vaccine or drug therapies. In genomes, they are not highly represented and are difficult to identify with experimental approaches. Several computational methods have been developed to discriminate TMBBs from other types of proteins. However, the best performing approaches have a high fraction of false positive predictions. Results: In this article, we introduce a new machine learning approach for TMBB detection based on N-to-1 Extreme Learning Machines that significantly outperforms previous methods achieving a Matthews correlation coefficient of 0.82, a probability of correct prediction of 0.92 and a sensitivity of 0.73. Availability: The method and the cross-validation sets are available at the web page http://betaware.biocomp.unibo.it/BetAware. Contact: piero.fariselli@unibo.i