ArticleMethods (San Diego, Calif.)2016
Advances in the molecular dynamics flexible fitting method for cryo-EM modeling.
Article in Methods (San Diego, Calif.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- Navigating bacterial motility through chemotaxis: from molecular mechanisms to physiological perspectives.Folia microbiologica · 2025Review
- A structural biology compatible file format for atomic force microscopy.Nature communications · 2025Article
- Article
- Connecting the dots: deep learning-based automated model building methods in cryo-EM.Frontiers in molecular biosciences · 2025Review
- 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
- Cryo-EM structure and B-factor refinement with ensemble representation.Nature communications · 2024Article
- Enhancing cryo-EM maps with 3D deep generative networks for assisting protein structure modeling.Bioinformatics (Oxford, England) · 2023Article
- Structural basis for control of bacterial RNA polymerase pausing by a riboswitch and its ligand.Nature structural & molecular biology · 2023Article
- Understanding Virus Structure and Dynamics through Molecular Simulations.Journal of chemical theory and computation · 2023Review
- Article
- Protein model refinement for cryo-EM maps using AlphaFold2 and the DAQ score.Acta crystallographica. Section D, Structural biology · 2023Article
- Mechanisms of E. coli chemotaxis signaling pathways visualized using cryoET and computational approaches.Biochemical Society transactions · 2022Review
- Geneticin shows selective antiviral activity against SARS-CoV-2 by interfering with programmed -1 ribosomal frameshifting.Antiviral research · 2022Article
- High-resolution reconstruction of a Jumbo-bacteriophage infecting capsulated bacteria using hyperbranched tail fibers.Nature communications · 2022Article
- Structural mechanism for bidirectional actin cross-linking by T-plastin.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Protein Structural Modeling for Electron Microscopy Maps Using VESPER and MAINMAST.Current protocols · 2022Article
- Sub-3-Å cryo-EM structure of RNA enabled by engineered homomeric self-assembly.Nature methods · 2022Article
- Probing Structural Perturbation of Biomolecules by Extracting Cryo-EM Data Heterogeneity.Biomolecules · 2022Review
- A hybrid approach to study large conformational transitions of biomolecules from single particle XFEL diffraction data.Frontiers in molecular biosciences · 2022Article
- Simulation and Machine Learning Methods for Ion-Channel Structure Determination, Mechanistic Studies and Drug Design.Frontiers in pharmacology · 2022Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Molecular Dynamics Flexible Fitting (MDFF) is an established technique for fitting all-atom structures of molecules into corresponding cryo-electron microscopy (cryo-EM) densities. The practical application of MDFF is simple but requires a user to be aware of and take measures against a variety of possible challenges presented by each individual case. Some of these challenges arise from the complexity of a molecular structure or the limited quality of available structural models and densities to be interpreted, while others stem from the intricacies of MDFF itself. The current article serves as an overview of the strategies that have been developed since MDFF's inception to overcome common challenges and successfully perform MDFF simulations.
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Registered trials
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