Integrative approach for detecting membrane proteins
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Integrative approach for detecting membrane proteins Munira Alballa1,2* and Gregory Butler1,3
From Joint NETTAB/BBCC 2019 Meeting - Network Tools and Applications in Biology (NETTAB) & Bioinformatics and Computational Biology Conference Salerno, Italy. 11-13 November 2019 *Correspondence: [email protected] 2 College of Computer and Information Sciences, King Saud University, Riyadh, Saudi Arabia Full list of author information is available at the end of the article
Abstract Background: 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. Results: 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 crossvalidation 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. Conclusion: 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-theart methods. Keywords: Membrane, Prediction model, Machine learning, Amino acid composition, Integral membrane proteins, Surface-bound membrane proteins, Transmembrane, Integrative approach
Background Membrane proteins play essential roles in transport, signaling, adhesion, and metabolism, which positions them as a leading drug target; over half of the current FDAapproved drugs target membrane proteins [1]. Membrane proteins are among the least characterized proteins in terms of their structure and function due to their hydrophobic surfaces and poor conformational stability. Distinguishing membrane proteins can help direct future experiments and provide clues regarding the functions of these proteins. © The Author(s) 2020. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If materi
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