Integrative approach for detecting membrane proteins

• Published in: BMC bioinformatics 2020-12, Vol.21 (Suppl 19), p.575-25, Article 575
• Main Authors: Alballa, Munira, Butler, Gregory
• Format: Article
• Language: English
• Subjects: Accuracy; Algorithms; Amino acid composition; Amino acids; Amino Acids - chemistry; Analysis; Area Under Curve; Databases, Protein; Datasets; Evaluation; Feature extraction; Integral membrane proteins; Learning algorithms; Lipids; Machine learning; Membrane; Membrane proteins; Membrane Proteins - chemistry; Membrane Proteins - metabolism; Membranes; Methods; Neural networks; Peptides; Position-Specific Scoring Matrices; Prediction model; Predictions; Proteins; ROC Curve; Support vector machines; Surface-bound membrane proteins; Topology
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-020-03891-x

Membrane proteins are key gates that control various vital cellular functions. Membrane proteins are often detected using transmembrane topology prediction tools. While transmembrane topology prediction tools can detect integral membrane proteins, they do not address surface-bound proteins. In this study, we focused on finding the best techniques for distinguishing all types of membrane proteins. This research first demonstrates the shortcomings of merely using transmembrane topology prediction tools to detect all types of membrane proteins. Then, the performance of various feature extraction techniques in combination with different machine learning algorithms was explored. The experimental results obtained by cross-validation and independent testing suggest that applying an integrative approach that combines the results of transmembrane topology prediction and position-specific scoring matrix (Pse-PSSM) optimized evidence-theoretic k nearest neighbor (OET-KNN) predictors yields the best performance. The integrative approach outperforms the state-of-the-art methods in terms of accuracy and MCC, where the accuracy reached a 92.51% in independent testing, compared to the 89.53% and 79.42% accuracies achieved by the state-of-the-art methods.