ArticleeLife2016
Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps.
Article in eLife, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 95 papers.
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Who cites it
95 citing papers in PubMed.
- Lenacapavir prevents production of infectious HIV-1 by abrogating immature virus assembly.bioRxiv : the preprint server for biology · 2026Article
- Transient protein structure guides surface diffusion pathways for electron transport in membrane supercomplexes.Nature communications · 2026Article
- Hydrogen Atomic Motions in Different Intramolecular Environments: HThe journal of physical chemistry letters · 2026Article
- Modeling cryo-EM structures in alternative states with AlphaFold2-based models and density-guided simulations.Communications chemistry · 2025Article
- Cryo-EM ligand building using AlphaFold3-like model and molecular dynamics.PLoS computational biology · 2025Article
- MELD in Action: Harnessing Data to Accelerate Molecular Dynamics.Journal of chemical information and modeling · 2025Review
- A structural biology compatible file format for atomic force microscopy.Nature communications · 2025Article
- AI-based methods for biomolecular structure modeling for Cryo-EM.Current opinion in structural biology · 2025Review
- 3D variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetase.Nature communications · 2024Article
- Structural mechanism of HP1⍺-dependent transcriptional repression and chromatin compaction.Structure (London, England : 1993) · 2024Article
- Protein complex structure modeling by cross-modal alignment between cryo-EM maps and protein sequences.Nature communications · 2024Article
- 3D Variability Analysis Reveals a Hidden Conformational Change Controlling Ammonia Transport in Human Asparagine Synthetase.bioRxiv : the preprint server for biology · 2024Article
- Bayesian reweighting of biomolecular structural ensembles using heterogeneous cryo-EM maps with the cryoENsemble method.Scientific reports · 2024Article
- Oligomerization and a distinct tRNA-binding loop are important regulators of human arginyl-transferase function.Nature communications · 2024Article
- GOLEM: Automated and Robust Cryo-EM-Guided Ligand Docking with Explicit Water Molecules.Journal of chemical information and modeling · 2024Article
- 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
- CombFold: predicting structures of large protein assemblies using a combinatorial assembly algorithm and AlphaFold2.Nature methods · 2024Article
- Cryo-EM structure and B-factor refinement with ensemble representation.Nature communications · 2024Article
- Predictive identification and design of potent inhibitors targeting resistance-inducing candidate genes fromFrontiers in bioinformatics · 2024Article
35 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
Two structure determination methods, based on the molecular dynamics flexible fitting (MDFF) paradigm, are presented that resolve sub-5 Å cryo-electron microscopy (EM) maps with either single structures or ensembles of such structures. The methods, denoted cascade MDFF and resolution exchange MDFF, sequentially re-refine a search model against a series of maps of progressively higher resolutions, which ends with the original experimental resolution. Application of sequential re-refinement enables MDFF to achieve a radius of convergence of ~25 Å demonstrated with the accurate modeling of β-galactosidase and TRPV1 proteins at 3.2 Å and 3.4 Å resolution, respectively. The MDFF refinements uniquely offer map-model validation and B-factor determination criteria based on the inherent dynamics of the macromolecules studied, captured by means of local root mean square fluctuations. The MDFF tools described are available to researchers through an easy-to-use and cost-effective cloud computing resource on Amazon Web Services.
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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.