ReviewJournal of chemical information and modeling2020
Simulation-Based Methods for Model Building and Refinement in Cryoelectron Microscopy.
Review in Journal of chemical information and modeling, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
13 citing papers in PubMed.
- From code to cure: computational identification of LasR inhibitors to combat quorum sensing in P. aeruginosa.Molecular diversity · 2026Article
- Toward a unifying mechanistic model of eukaryotic translation initiation through integrative single-molecule, structural, and computational insights.Current opinion in structural biology · 2026Review
- Ensemble refinement of mismodeled cryo-EM RNA structures using all-atom simulations.Nature communications · 2025Article
- Navigating the unstructured by evaluating alphafold's efficacy in predicting missing residues and structural disorder in proteins.PloS one · 2025Article
- Dynamic conformational switching underlies TFIIH function in transcription and DNA repair and impacts genetic diseases.Nature communications · 2023Article
- Mesoscience in cell biology and cancer research.Cancer innovation · 2022Review
- Application of BIM Technology in Prefabricated Buildings Based on Virtual Reality.Computational intelligence and neuroscience · 2022Article
- Mechanism of Rad26-assisted rescue of stalled RNA polymerase II in transcription-coupled repair.Nature communications · 2021Article
- Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps.Journal of chemical information and modeling · 2021Article
- How proteins open fusion pores: insights from molecular simulations.European biophysics journal : EBJ · 2021Review
- Intelligent Building Construction Management Based on BIM Digital Twin.Computational intelligence and neuroscience · 2021Article
- Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules.Frontiers in molecular biosciences · 2021Article
- Faces of Contemporary CryoEM Information and Modeling.Journal of chemical information and modeling · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Advances in cryoelectron microscopy (cryo-EM) have revolutionized the structural investigation of large macromolecular assemblies. In this review, we first provide a broad overview of modeling methods used for flexible fitting of molecular models into cryo-EM density maps. We give special attention to approaches rooted in molecular simulations-atomistic molecular dynamics and Monte Carlo. Concise descriptions of the methods are given along with discussion of their advantages, limitations, and most popular alternatives. We also describe recent extensions of the widely used molecular dynamics flexible fitting (MDFF) method and discuss how different model-building techniques could be incorporated into new hybrid modeling schemes and simulation workflows. Finally, we provide two illustrative examples of model-building and refinement strategies employing MDFF, cascade MDFF, and RosettaCM. These examples come from recent cryo-EM studies that elucidated transcription preinitiation complexes and shed light on the functional roles of these assemblies in gene expression and gene regulation.
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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.