ArticleProceedings. IEEE International Conference on Bioinformatics and Biomedicine2022
Refinement of AlphaFold2 Models against Experimental Cryo-EM Density Maps at 4-6Å Resolution.
Article in Proceedings. IEEE International Conference on Bioinformatics and Biomedicine, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Flexible fitting of AlphaFold2-predicted models to cryo-EM density maps using elastic network models: a methodical affirmation.Bioinformatics advances · 2025Article
- Decoys Reveal Multiple Basins of Attraction for Cryo-Electron-Microscopy Flexible Fitting.Computational structural bioinformatics : international workshop, CSBW 2024, Boston, MA, USA, November 16, 2024, proceedings. Computational Structural Bioinformatics Workshop (2024 : Boston, Mass.) · 2025Article
- AlphaFold2 Model Refinement Using Structure Decoys.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2023Article
- Novel Artificial Intelligence-Based Approaches for Ab Initio Structure Determination and Atomic Model Building for Cryo-Electron Microscopy.Micromachines · 2023Review
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Authors and funding
3 authors.
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Abstract
This work provides new evidence of the utility of deep learning-based protein structure prediction approaches, specifically AlphaFold2, in the interpretation of 4-6 Å resolution cryo-EM maps. We describe the dependencies, as well as the strengths and limitations, of integrating experimental and AI-based approaches to building accurate models, even from poorly resolved density maps. The test followed recent work that implemented a refinement protocol in the Phenix program, which successfully refined AlphaFold2 models in high-resolution maps but which at lower resolution relied on simulated "hybrid density maps". To study the noise and imperfections present in experimental cryo-EM maps more realistically, in this work, we selected only experimental map/model pairs in the 4-6 Å resolution range where refinement performance starts to degrade. Most of the AlphaFold2 predicted models are highly accurate, particularly for the 9 larger chains (226-373 residues long) of the 10 cases, exhibiting TM-scores above 0.9. A small chain of 115 residues in length containing three helices was poorly predicted, with a TM-score of 0.52. The observed success of the subsequent refinement step depends significantly on the quality of the AlphaFold2 prediction, the quality of the experimental cryo-EM data, and the quality of the alignment of the model with the density.
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