ArticleNature methods2024
DiffModeler: large macromolecular structure modeling for cryo-EM maps using a diffusion model.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed.
- Computational Approaches for Protein-DNA/RNA Complex Modeling for Cryo-EM Maps.Current protocols · 2026Article
- AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network.Nature methods · 2026Article
- Accurate Macromolecular Complex Modeling for Cryo-EM with CryoZeta.bioRxiv : the preprint server for biology · 2026Article
- CryoAtom improves model building for cryo-EM.Nature structural & molecular biology · 2026Article
- Fine-tuning AlphaFold with limited cryo-EM observations.Communications chemistry · 2026Article
- AlphaFold-RandomWalk and AlphaFold-Ensemble: Sampling Alternative Protein Conformations with Perturbed Versions of AlphaFold.Journal of chemical information and modeling · 2026Article
- pH-stimuli-responsive doxorubicin release and stability in chitosan-Eudragit nanocarriers.Scientific reports · 2025Article
- Structural insights into MERS and SARS coronavirus membrane proteins.Communications biology · 2025Article
- ACGA a Novel Biomimetic Hybrid Optimisation Algorithm Based on a HP Protein Visualizer: An Interpretable Web-Based Tool for 3D Protein Folding Based on the Hydrophobic-Polar Model.Biomimetics (Basel, Switzerland) · 2025Article
- Mettl15-Mettl17 modulates the transition from early to late pre-mitoribosome.Structure (London, England : 1993) · 2025Article
- Unraveling the Obesogenic Mechanism of Bisphenol A Through Network Toxicology and Molecular Docking: Identification of Key Molecular Targets.International journal of molecular sciences · 2025Article
- Distance-AF improves predicted protein structure models by AlphaFold2 with user-specified distance constraints.Communications biology · 2025Article
- Accurate Protein Dynamic Conformational Ensembles: Combining AlphaFold, MD, and AmideInternational journal of molecular sciences · 2025Article
- DEMO-EMol: modeling protein-nucleic acid complex structures from cryo-EM maps by coupling chain assembly with map segmentation.Nucleic acids research · 2025Article
- A comprehensive survey and benchmark of deep learning-based methods for atomic model building from cryo-electron microscopy density maps.Briefings in bioinformatics · 2025Article
- Article
- Finding antibodies in cryo-EM maps with CrAI.Bioinformatics (Oxford, England) · 2025Article
- Advancing structure modeling from cryo-EM maps with deep learning.Biochemical Society transactions · 2025Review
- AI-based methods for biomolecular structure modeling for Cryo-EM.Current opinion in structural biology · 2025Review
- Connecting the dots: deep learning-based automated model building methods in cryo-EM.Frontiers in molecular biosciences · 2025Review
Corrections and comments
- Update of
Authors and funding
5 authors.
Funding
Abstract
Cryogenic electron microscopy (cryo-EM) has now been widely used for determining multichain protein complexes. However, modeling a large complex structure, such as those with more than ten chains, is challenging, particularly when the map resolution decreases. Here we present DiffModeler, a fully automated method for modeling large protein complex structures. DiffModeler employs a diffusion model for backbone tracing and integrates AlphaFold2-predicted single-chain structures for structure fitting. DiffModeler showed an average template modeling score of 0.88 and 0.91 for two datasets of cryo-EM maps of 0-5 Å resolution and 0.92 for intermediate resolution maps (5-10 Å), substantially outperforming existing methodologies. Further benchmarking at low resolutions (10-20 Å) confirms its versatility, demonstrating plausible performance.
Indexed as
Identifiers
What OpenQuestion holds
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.