| Abstrakt: |
Simple Summary: Phosphorylation is a crucial process that regulates various cellular activities. Detecting phosphorylation sites, especially in cells infected by the SARS-CoV-2 virus, is challenging due to technical limitations. To address this, we developed GBMPhos, an advanced tool combining deep learning techniques, to accurately identify these sites. GBMPhos outperformed traditional methods and current state-of-the-art approaches in identifying phosphorylation sites. We have developed a free web server, which helps researchers gain a better understanding of protein modifications during a SARS-CoV-2 infection, potentially aiding in the development of therapeutic strategies and contributing to the fight against COVID-19. Phosphorylation, a reversible and widespread post-translational modification of proteins, is essential for numerous cellular processes. However, due to technical limitations, large-scale detection of phosphorylation sites, especially those infected by SARS-CoV-2, remains a challenging task. To address this gap, we propose a method called GBMPhos, a novel method that combines convolutional neural networks (CNNs) for extracting local features, gating mechanisms to selectively focus on relevant information, and a bi-directional gated recurrent unit (Bi-GRU) to capture long-range dependencies within protein sequences. GBMPhos leverages a comprehensive set of features, including sequence encoding, physicochemical properties, and structural information, to provide an in-depth analysis of phosphorylation sites. We conducted an extensive comparison of GBMPhos with traditional machine learning algorithms and state-of-the-art methods. Experimental results demonstrate the superiority of GBMPhos over existing methods. The visualization analysis further highlights its effectiveness and efficiency. Additionally, we have established a free web server platform to help researchers explore phosphorylation in SARS-CoV-2 infections. The source code of GBMPhos is publicly available on GitHub. [ABSTRACT FROM AUTHOR] |
