ArticleNature methods2024
DynaMight: estimating molecular motions with improved reconstruction from cryo-EM images.
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 51 papers.
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Who cites it
51 citing papers in PubMed.
- CryoROLE: describing large inter-domain rotation in single particle cryo-EM.bioRxiv : the preprint server for biology · 2026Article
- Structural basis of the regulation by CDK11 kinase of early spliceosome activation and evidence for its proofreading by DHX15 helicase.Nature communications · 2026Article
- Digital twin of biomacromolecular thermodynamics in cryo-EM data.Communications chemistry · 2026Article
- The E. coli DnaX clamp loader sharply bends DNA to load β-clamp at nicks and small gaps.Molecular cell · 2026Article
- Applications and prospects of cryo-electron tomography in drug discovery and understanding disease.Current opinion in structural biology · 2026Review
- Article
- Heterogeneous reconstruction algorithms for cryoEM achieve limited particle classification accuracy on real benchmark datasets.bioRxiv : the preprint server for biology · 2026Article
- Advances in cryo-EM that have shaped mechanistic models of membrane-attack-complex assembly and regulation.IUCrJ · 2026Review
- Breaking barriers: transitioning from X-ray crystallography to cryo-EM for structural studies.Acta crystallographica. Section D, Structural biology · 2026Article
- CryoJAX: a cryo-electron microscopy image-simulation library in JAX.Acta crystallographica. Section D, Structural biology · 2026Article
- Multimodal learning on heterogeneous subgraphs and LLMs representation for MHC-peptide binding affinity prediction.BMC bioinformatics · 2026Article
- Point cloud deformation modeling for particle selection following cryo-EM 2D classification.BMC bioinformatics · 2026Article
- Curvy Surface Reconstruction.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Integrated experimental and AI innovations for RNA structure determination.Nature biotechnology · 2026Review
- MacroH2A-Mediated Gene Repression through Nucleosome Compaction and Remodeling Inhibition.bioRxiv : the preprint server for biology · 2026Article
- Article
- ThebioRxiv : the preprint server for biology · 2026Article
- The Open Conformation of CCT: How to Achieve High Resolution Using CryoEM.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Comparing cryo-EM methods and molecular dynamics simulation to investigate heterogeneity in ligand-bound TRPV1.Nature communications · 2025Article
- Cryo-electron microscopy ensemble optimization using individual particles and physical constraints.bioRxiv : the preprint server for biology · 2025Article
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5 authors.
Funding
Abstract
How to deal with continuously flexing molecules is one of the biggest outstanding challenges in single-particle analysis of proteins from cryogenic-electron microscopy (cryo-EM) images. Here, we present DynaMight, a software tool that estimates a continuous space of conformations in a cryo-EM dataset by learning three-dimensional deformations of a Gaussian pseudo-atomic model of a consensus structure for every particle image. Inversion of the learned deformations is then used to obtain an improved reconstruction of the consensus structure. We illustrate the performance of DynaMight for several experimental cryo-EM datasets. We also show how error estimates on the deformations may be obtained by independently training two variational autoencoders on half sets of the cryo-EM data, and how regularization of the three-dimensional deformations through the use of atomic models may lead to important artifacts due to model bias. DynaMight is distributed as free, open-source software, as part of RELION-5.
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