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Medium-resolution cryo-electron microscopy (cryo-EM) density maps preserve substantial information about protein secondary-structure organization; however, accurately recovering the topology and connectivity of α-helices and β-strands remains challenging due to noise, structural heterogeneity, and the intrinsic resolution limitations that obscure residue-level detail. Topology determination is a key intermediate step toward building atomic protein models from medium-resolution cryo-EM density maps. It requires identifying the correct correspondence and orientation between secondary-structure elements (SSEs), i.e., α-helices and β-strands, predicted from the amino-acid sequence and those detected in the three dimensional (3D) density map. Despite significant advances in cryo-EM reconstruction and molecular modelling, this correspondence problem remains a challenging task, particularly in the presence of noisy density maps and in large, topologically complex α/β proteins. To address this issue, we propose a fully automated, classification-based framework that infers protein secondary-structure topology directly from medium-resolution cryo-EM density maps. Specifically, we cast topology determination as a supervised classification problem in three-dimensional space, leveraging geometric learning on model-derived Cα coordinate representations to establish SSE correspondences, and a Dynamic Time Warping (DTW)-based procedure to resolve density-stick directionality. Validation on a benchmark of 38 proteins spanning both simulated and experimental cryo-EM maps and covering diverse fold classes (α, β, and α/β) demonstrates strong and consistent performance. Among the evaluated predictors, the Voronoi (1-NN) classifier achieves the highest average correspondence quality, with a mean F1-score of 96.82% across the full benchmark. The framework also scales to large, topologically dense targets containing up to 65 secondary-structure elements while preserving very fast correspondence inference (<3 ms), offering a substantial improvement over prior baselines in both accuracy and computational cost. Overall, the classification-driven strategy provides reliable SSE-to-density matching and, when coupled with DTW-based direction selection, yields stronger topology constraints that directly support model building and refinement from medium-resolution cryo-EM reconstructions, while remaining easy to integrate into existing structural interpretation pipelines.
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Deep Learning Approach to Identify Protein’s Secondary Structure Elements
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.
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- Award ID(s):
- 2153807
- PAR ID:
- 10541118
- Publisher / Repository:
- Springer, Singapore
- Date Published:
- Volume:
- 14954
- ISBN:
- 978-981-97-5128-0
- Subject(s) / Keyword(s):
- Protein Modeling Protein Secondary Structure Elements Deep Learning Cryo-EM Map Inception Architecture Machine Learning
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract The breakthrough in cryo-electron microscopy (cryo-EM) technology has led to an increasing number of density maps of biological macromolecules. However, constructing accurate protein complex atomic structures from cryo-EM maps remains a challenge. In this study, we extend our previously developed DEMO-EM to present DEMO-EM2, an automated method for constructing protein complex models from cryo-EM maps through an iterative assembly procedure intertwining chain- and domain-level matching and fitting for predicted chain models. The method was carefully evaluated on 27 cryo-electron tomography (cryo-ET) maps and 16 single-particle EM maps, where DEMO-EM2 models achieved an average TM-score of 0.92, outperforming those of state-of-the-art methods. The results demonstrate an efficient method that enables the rapid and reliable solution of challenging cryo-EM structure modeling problems.more » « less
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Cryo-electron microscopy (cryo-EM) is a structural technique that has played a significant role in protein structure determination in recent years. Compared to the traditional methods of X-ray crystallography and NMR spectroscopy, cryo-EM is capable of producing images of much larger protein complexes. However, cryo-EM reconstructions are limited to medium-resolution (~4–10 Å) for some cases. At this resolution range, a cryo-EM density map can hardly be used to directly determine the structure of proteins at atomic level resolutions, or even at their amino acid residue backbones. At such a resolution, only the position and orientation of secondary structure elements (SSEs) such as α-helices and β-sheets are observable. Consequently, finding the mapping of the secondary structures of the modeled structure (SSEs-A) to the cryo-EM map (SSEs-C) is one of the primary concerns in cryo-EM modeling. To address this issue, this study proposes a novel automatic computational method to identify SSEs correspondence in three-dimensional (3D) space. Initially, through a modeling of the target sequence with the aid of extracting highly reliable features from a generated 3D model and map, the SSEs matching problem is formulated as a 3D vector matching problem. Afterward, the 3D vector matching problem is transformed into a 3D graph matching problem. Finally, a similarity-based voting algorithm combined with the principle of least conflict (PLC) concept is developed to obtain the SSEs correspondence. To evaluate the accuracy of the method, a testing set of 25 experimental and simulated maps with a maximum of 65 SSEs is selected. Comparative studies are also conducted to demonstrate the superiority of the proposed method over some state-of-the-art techniques. The results demonstrate that the method is efficient, robust, and works well in the presence of errors in the predicted secondary structures of the cryo-EM images.more » « less
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