ArticleNature methods2022
Improved AlphaFold modeling with implicit experimental information.
Article in Nature methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers.
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Who cites it
84 citing papers in PubMed, 132 citations in OpenAlex.
- Predicting RNA and Protein:RNA Complexes with AlphaFold: Possibilities, Limitations, and Practical Guidelines.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Functional and structural basis of Omicron BA.3.2.1 spike.Cell reports · 2026Article
- EMReady2: improvement of cryo-EM and cryo-ET maps by local quality-aware deep learning with Mamba.Nature communications · 2026Article
- Hidden structural states of proteins revealed by conformer selection.Nature communications · 2026Article
- Experimental Data Driven AI Framework for Flexible Protein Conformational Reconstruction.bioRxiv : the preprint server for biology · 2026Article
- Structural basis for the recruitment and selective phosphorylation of Akt by mTORC2.Science (New York, N.Y.) · 2026Article
- Guiding AlphaFold predictions with experimental knowledge to inform dynamics and interactions with VAIRO.Protein science : a publication of the Protein Society · 2026Article
- EMProt improves structure determination from cryo-EM maps.Nature structural & molecular biology · 2026Article
- Practical Outcomes From CASP16 for Users in Need of Biomolecular Structure Prediction.Proteins · 2026Review
- Bisphenols-enhanced platelet aggregation via TP, P2YFrontiers in pharmacology · 2026Article
- MISO: microfluidic protein isolation enables single-particle cryo-EM structure determination from a single cell colony.Nature methods · 2025Article
- Combining Cryo-EM with Computational Approaches To Revolutionize Structural Biology.The protein journal · 2025Review
- Structure of an LGR dimer, an evolutionary predecessor of glycoprotein hormone receptors.Nature communications · 2025Article
- Molecular mechanism and structural models of protein-mediated copper transfer to the Arabidopsis thaliana ethylene receptor ETR1 at the ER membrane.Scientific reports · 2025Article
- Modeling cryo-EM structures in alternative states with AlphaFold2-based models and density-guided simulations.Communications chemistry · 2025Article
- Article
- Deep-learning structure elucidation from single-mutant deep mutational scanning.Nature communications · 2025Article
- AlphaFold-guided structural analyses of nucleosome binding proteins.Nucleic acids research · 2025Article
- Assisting and accelerating NMR assignment with restrained structure prediction.Communications biology · 2025Article
- The dimerization domain of SARS-CoV-2 nucleocapsid protein is partially disordered and forms a dynamic high-affinity dimer.Cell reports. Physical science · 2025Article
24 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 4 institutions in 2 countries.
Funding
Abstract
Machine-learning prediction algorithms such as AlphaFold and RoseTTAFold can create remarkably accurate protein models, but these models usually have some regions that are predicted with low confidence or poor accuracy. We hypothesized that by implicitly including new experimental information such as a density map, a greater portion of a model could be predicted accurately, and that this might synergistically improve parts of the model that were not fully addressed by either machine learning or experiment alone. An iterative procedure was developed in which AlphaFold models are automatically rebuilt on the basis of experimental density maps and the rebuilt models are used as templates in new AlphaFold predictions. We show that including experimental information improves prediction beyond the improvement obtained with simple rebuilding guided by the experimental data. This procedure for AlphaFold modeling with density has been incorporated into an automated procedure for interpretation of crystallographic and electron cryo-microscopy maps.
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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.