ArticleBMC structural biology2018
Accurate flexible refinement of atomic models against medium-resolution cryo-EM maps using damped dynamics.
Article in BMC structural biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- EMProt improves structure determination from cryo-EM maps.Nature structural & molecular biology · 2026Article
- Centriolar cap proteins CP110 and CPAP control slow elongation of microtubule plus ends.The Journal of cell biology · 2025Article
- Toward Modeling Protein Multimers by Combining AlphaFold 3 Predictions with Secondary Structures from Medium-Resolution Cryo-EM Maps.Computational structural bioinformatics : international workshop, CSBW 2024, Boston, MA, USA, November 16, 2024, proceedings. Computational Structural Bioinformatics Workshop (2024 : Boston, Mass.) · 2025Article
- Flexible fitting of AlphaFold2-predicted models to cryo-EM density maps using elastic network models: a methodical affirmation.Bioinformatics advances · 2025Article
- The combined focal loss and dice loss function improves the segmentation of beta-sheets in medium-resolution cryo-electron-microscopy density maps.Bioinformatics advances · 2024Article
- Structure ofViruses · 2023Article
- Fostering discoveries in the era of exascale computing: How the next generation of supercomputers empowers computational and experimental biophysics alike.Biophysical journal · 2023Review
- eIF4A1-dependent mRNAs employ purine-rich 5'UTR sequences to activate localised eIF4A1-unwinding through eIF4A1-multimerisation to facilitate translation.Nucleic acids research · 2023Article
- Refinement of AlphaFold2 Models against Experimental Cryo-EM Density Maps at 4-6Å Resolution.Proceedings. IEEE International Conference on Bioinformatics and Biomedicine · 2022Article
- CR-I-TASSER: assemble protein structures from cryo-EM density maps using deep convolutional neural networks.Nature methods · 2022Article
- Refinement of AlphaFold2 models against experimental and hybrid cryo-EM density maps.QRB discovery · 2022Article
- Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome.Nature structural & molecular biology · 2021Article
- Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules.Frontiers in molecular biosciences · 2021Article
- A New Protocol for Atomic-Level Protein Structure Modeling and Refinement Using Low-to-Medium Resolution Cryo-EM Density Maps.Journal of molecular biology · 2020Article
- Deep learning enables the atomic structure determination of the Fanconi Anemia core complex from cryoEM.IUCrJ · 2020Article
- Structural Biology in the Multi-Omics Era.Journal of chemical information and modeling · 2020Article
- An asymmetric sheath controls flagellar supercoiling and motility in the leptospira spirochete.eLife · 2020Article
- Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps.Molecules (Basel, Switzerland) · 2019Review
- Frontiers in CryoEM Modeling.Journal of chemical information and modeling · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
backgroundDramatic progress has recently been made in cryo-electron microscopy technologies, which now make possible the reconstruction of a growing number of biomolecular structures to near-atomic resolution. However, the need persists for fitting and refinement approaches that address those cases that require modeling assistance.
methodsIn this paper, we describe algorithms to optimize the performance of such medium-resolution refinement methods. These algorithms aim to automatically optimize the parameters that define the density shape of the flexibly fitted model, as well as the time-dependent damper cutoff distance. Atomic distance constraints can be prescribed for cases where extra containment of parts of the structure is helpful, such as in regions where the density map is poorly defined. Also, we propose a simple stopping criterion that estimates the probable onset of overfitting during the simulation.
resultsThe new set of algorithms produce more accurate fitting and refinement results, and yield a faster rate of convergence of the trajectory toward the fitted conformation. The latter is also more reliable due to the overfitting warning provided to the user.
conclusionsThe algorithms described here were implemented in the new Damped-Dynamics Flexible Fitting simulation tool "DDforge" in the Situs package.
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