ArticleiScience2022
AlphaFold2 and CryoEM: Revisiting CryoEM modeling in near-atomic resolution density maps.
Article in iScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Enhancing Caffeic Acid Production inMetabolites · 2026Article
- Structural basis for RNA-guided DNA degradation by Cas5-HNH/Cascade complex.Nature communications · 2025Article
- Bridging prediction and reality: Comprehensive analysis of experimental and AlphaFold 2 full-length nuclear receptor structures.Computational and structural biotechnology journal · 2025Article
- Modular Structure and Polymerization Status of GABAInternational journal of molecular sciences · 2024Article
- The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins.Nature chemical biology · 2024Review
- A predicted model-aided reconstruction algorithm for X-ray free-electron laser single-particle imaging.IUCrJ · 2024Article
- Predictive modeling and cryo-EM: A synergistic approach to modeling macromolecular structure.Biophysical journal · 2024Review
- Cysteine and homocysteine can be exploited by GPX4 in ferroptosis inhibition independent of GSH synthesis.Redox biology · 2024Article
- The advent of preventive high-resolution structural histopathology by artificial-intelligence-powered cryogenic electron tomography.Frontiers in molecular biosciences · 2024Review
- Integrating machine learning to advance epitope mapping.Frontiers in immunology · 2024Review
- AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination.Nature methods · 2024Article
- DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction.Nature methods · 2024Article
- AlphaFold, allosteric, and orthosteric drug discovery: Ways forward.Drug discovery today · 2023Review
- Exploring AlphaFold2's Performance on Predicting Amino Acid Side-Chain Conformations and Its Utility in Crystal Structure Determination of B318L Protein.International journal of molecular sciences · 2023Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
With the advent of new artificial intelligence and machine learning algorithms, predictive modeling can, in some cases, produce structures on par with experimental methods. The combination of predictive modeling and experimental structure determination by electron cryomicroscopy (cryoEM) offers a tantalizing approach for producing robust atomic models of macromolecular assemblies. Here, we apply AlphaFold2 to a set of community standard data sets and compare the results with the corresponding reference maps and models. Moreover, we present three unique case studies from previously determined cryoEM density maps of viruses. Our results show that AlphaFold2 can not only produce reasonably accurate models for analysis and additional hypotheses testing, but can also potentially yield incorrect structures if not properly validated with experimental data. Whereas we outline numerous shortcomings and potential pitfalls of predictive modeling, the obvious synergy between predictive modeling and cryoEM will undoubtedly result in new computational modeling tools.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.