ArticleNature communications2021
VESPER: global and local cryo-EM map alignment using local density vectors.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 28 citations in OpenAlex.
- Computational Approaches for Protein-DNA/RNA Complex Modeling for Cryo-EM Maps.Current protocols · 2026Article
- Direct Detection and Atomic Modeling of Ligands in Cryo-EM Maps Using Deep Learning.bioRxiv : the preprint server for biology · 2026Article
- Accurate Macromolecular Complex Modeling for Cryo-EM with CryoZeta.bioRxiv : the preprint server for biology · 2026Article
- CryoAlign2: efficient global and local Cryo-EM map retrieval based on parallel-accelerated local spatial structural features.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
- Secondary Structure Detection and Structure Modeling for Cryo-EM.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Protein Secondary Structure and DNA/RNA Detection for Cryo-EM and Cryo-ET Using Emap2sec and Emap2secMethods in molecular biology (Clifton, N.J.) · 2025Article
- Connecting the dots: deep learning-based automated model building methods in cryo-EM.Frontiers in molecular biosciences · 2025Review
- DiffModeler: large macromolecular structure modeling for cryo-EM maps using a diffusion model.Nature methods · 2024Article
- DomainFit: Identification of protein domains in cryo-EM maps at intermediate resolution using AlphaFold2-predicted models.Structure (London, England : 1993) · 2024Article
- DiffModeler: Large Macromolecular Structure Modeling in Low-Resolution Cryo-EM Maps Using Diffusion Model.bioRxiv : the preprint server for biology · 2024Article
- Accurate global and local 3D alignment of cryo-EM density maps using local spatial structural features.Nature communications · 2024Article
- DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction.Nature methods · 2024Article
- Alignment of density maps in Wasserstein distance.Biological imaging · 2024Article
- Integrated Protocol of Protein Structure Modeling for Cryo-EM with Deep Learning and Structure Prediction.bioRxiv : the preprint server for biology · 2023Article
- Model building of protein complexes from intermediate-resolution cryo-EM maps with deep learning-guided automatic assembly.Nature communications · 2022Article
- Protein Structural Modeling for Electron Microscopy Maps Using VESPER and MAINMAST.Current protocols · 2022Article
- Real-time structure search and structure classification for AlphaFold protein models.Communications biology · 2022Article
- MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field.Frontiers in molecular biosciences · 2022Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
An increasing number of density maps of biological macromolecules have been determined by cryo-electron microscopy (cryo-EM) and stored in the public database, EMDB. To interpret the structural information contained in EM density maps, alignment of maps is an essential step for structure modeling, comparison of maps, and for database search. Here, we developed VESPER, which captures the similarity of underlying molecular structures embedded in density maps by taking local gradient directions into consideration. Compared to existing methods, VESPER achieved substantially more accurate global and local alignment of maps as well as database retrieval.
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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.