Assigning secondary structure in proteins using AI

Knowledge about protein structure assignment enriches the structural and functional understanding of proteins. Accurate and reliable structure assignment data is crucial for secondary structure prediction systems. Since the 1980s, various methods based on hydrogen bond analysis and atomic coordinate geometry, followed by machine learning, have been employed in protein structure assignment. However, the assignment process becomes challenging when missing atoms are present in the protein files. Our method proposed a multi-class classifier program named DLFSA for assigning protein secondary structure elements (SSE) using convolutional neural networks (CNNs). A fast and efficient GPU-based parallel procedure extracts fragments from protein files. The model implemented in this work is trained with a subset of the protein fragments and achieves 88.1% and 82.5% train and test accuracy, respectively. The model uses only C_α coordinates for secondary structure assignments. The model has been successfully tested on a few full-length proteins also. Results from the fragment-based studies demonstrate the feasibility of applying deep learning solutions for structure assignment problems.