ArticleeLife2019
Automated cryo-EM structure refinement using correlation-driven molecular dynamics.
Article in eLife, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
What it found
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Who cites it
49 citing papers in PubMed.
- Best for the Eye, Not for the Algorithm: Anisotropy in Fitting Atomic Models in Cryo-EM.bioRxiv : the preprint server for biology · 2026Article
- KNexPHENIX: A PHENIX-Based Workflow for Improving Cryo-EM and Crystallographic Structural Models.Journal of chemical information and modeling · 2026Article
- Inducible CD147 up-regulation boosts extended SARS-CoV-2 infection triggering severe COVID-19 independent of ACE2.Signal transduction and targeted therapy · 2026Article
- Cryo-electron microscopy ensemble optimization using individual particles and physical constraints.bioRxiv : the preprint server for biology · 2025Article
- Modeling cryo-EM structures in alternative states with AlphaFold2-based models and density-guided simulations.Communications chemistry · 2025Article
- KNexPHENIX: A PHENIX-Based Workflow for Improving Cryo-EM and Crystallographic Structural Models.bioRxiv : the preprint server for biology · 2025Article
- An Empirical Biasing Force Constant to Minimize Overfitting in Cryo-EM Flexible Fitting Refinement.Journal of chemical information and modeling · 2025Article
- Cryo-EM ligand building using AlphaFold3-like model and molecular dynamics.PLoS computational biology · 2025Article
- Activity of botulinum neurotoxin X and its structure when shielded by a non-toxic non-hemagglutinin protein.Communications chemistry · 2024Article
- Bayesian reweighting of biomolecular structural ensembles using heterogeneous cryo-EM maps with the cryoENsemble method.Scientific reports · 2024Article
- Pathways to a Shiny Future: Building the Foundation for Computational Physical Chemistry and Biophysics in 2050.ACS physical chemistry Au · 2024Review
- MDFF_NM: Improved Molecular Dynamics Flexible Fitting into Cryo-EM Density Maps with a Multireplica Normal Mode-Based Search.Journal of chemical information and modeling · 2024Article
- Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.Nature methods · 2024Article
- Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference.PLoS computational biology · 2024Article
- Cryo-EM structure and B-factor refinement with ensemble representation.Nature communications · 2024Article
- Conformational plasticity and allosteric communication networks explain Shelterin protein TPP1 binding to human telomerase.Communications chemistry · 2023Article
- Automated simulation-based membrane protein refinement into cryo-EM data.Biophysical journal · 2023Article
- Gentle and fast all-atom model refinement to cryo-EM densities via a maximum likelihood approach.PLoS computational biology · 2023Article
- MDTOMO method for continuous conformational variability analysis in cryo electron subtomograms based on molecular dynamics simulations.Scientific reports · 2023Article
- The IgG4 hinge with CD28 transmembrane domain improves VNature communications · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
We present a correlation-driven molecular dynamics (CDMD) method for automated refinement of atomistic models into cryo-electron microscopy (cryo-EM) maps at resolutions ranging from near-atomic to subnanometer. It utilizes a chemically accurate force field and thermodynamic sampling to improve the real-space correlation between the modeled structure and the cryo-EM map. Our framework employs a gradual increase in resolution and map-model agreement as well as simulated annealing, and allows fully automated refinement without manual intervention or any additional rotamer- and backbone-specific restraints. Using multiple challenging systems covering a wide range of map resolutions, system sizes, starting model geometries and distances from the target state, we assess the quality of generated models in terms of both model accuracy and potential of overfitting. To provide an objective comparison, we apply several well-established methods across all examples and demonstrate that CDMD performs best in most cases.
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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.