PredβTM: A Novel β-Transmembrane Region Prediction Algorithm

• Published in: PloS one Vol. 10; no. 12; p. e0145564
• Main Authors: Roy Choudhury, Amrita, Novič, Marjana
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 22.12.2015; Public Library of Science (PLoS)
• Subjects: Acids; Algorithms; Amino acid sequence; Amino acids; Bacteria; Bioinformatics; Gene sequencing; Genomes; Gram-positive bacteria; Laboratories; Membrane proteins; Membrane Proteins - chemistry; Membrane Proteins - genetics; Predictions; Predictive Value of Tests; Protein Structure, Secondary; Protein Structure, Tertiary; Proteins; Segments; Sensitivity; Sensitivity analysis; Sequence Analysis, Protein - methods; Slovenia
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0145564

Predicting the transmembrane regions is an important aspect of understanding the structures and architecture of different β-barrel membrane proteins. Despite significant efforts, currently available β-transmembrane region predictors are still limited in terms of prediction accuracy, especially in precision. Here, we describe PredβTM, a transmembrane region prediction algorithm for β-barrel proteins. Using amino acid pair frequency information in known β-transmembrane protein sequences, we have trained a support vector machine classifier to predict β-transmembrane segments. Position-specific amino acid preference data is incorporated in the final prediction. The predictor does not incorporate evolutionary profile information explicitly, but is based on sequence patterns generated implicitly by encoding the protein segments using amino acid adjacency matrix. With a benchmark set of 35 β-transmembrane proteins, PredβTM shows a sensitivity and precision of 83.71% and 72.98%, respectively. The segment overlap score is 82.19%. In comparison with other state-of-art methods, PredβTM provides a higher precision and segment overlap without compromising with sensitivity. Further, we applied PredβTM to analyze the β-barrel membrane proteins without defined transmembrane regions and the uncharacterized protein sequences in eight bacterial genomes and predict possible β-transmembrane proteins. PredβTM can be freely accessed on the web at http://transpred.ki.si/.