Deep Learning Approach to Identify Protein’s Secondary Structure Elements

Cryo-electron microscopy (cryo-EM) has become a crucial method for structure determination. Despite the substantial growth in deposited cryo-EM maps driven by advances in microscopy and image processing, accurately constructing models from these maps remains challenging. Extracting secondary structure information from EM maps is valuable for cryo-EM modeling. In this context, we introduce a novel deep learning secondary structure annotation framework specifically designed for intermediate-resolution cryo-EM maps, employing a three-dimensional Inception architecture. Testing it on diverse datasets, including maps with authentic intermediate resolutions, demonstrates its accuracy and robustness in identifying secondary structures in cryo-EM maps. We conducted a comparative analysis of our results against frameworks that exist in the state-of-the-art, and our framework demonstrated superior performance across nearly all secondary structure elements. We employed the F1 accuracy metric, yielding an average F1 score of 0.657 for helix, 0.712 for coil, and 0.596 for sheet predictions. Notably, certain helix and sheet predictions achieved an impressive F1 score of 0.881.