ArticleJournal of structural biology2019
Cryo_fit: Democratization of flexible fitting for cryo-EM.
Article in Journal of structural biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 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
- Mechanism of beta-arrestin 1 mediated Src activation via Src SH3 domain revealed by cryo-electron microscopy.Nature communications · 2026Article
- Fine-tuning AlphaFold with limited cryo-EM observations.Communications chemistry · 2026Article
- Cryo-EM structure of the Rift Valley fever virus envelope protein in complex with a potent neutralization antibody.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Structural dynamics of dengue virus UTRs and their cyclization.Biophysical journal · 2025Article
- Modeling cryo-EM structures in alternative states with AlphaFold2-based models and density-guided simulations.Communications chemistry · 2025Article
- Mechanism of beta-arrestin 1 mediated Src activation via Src SH3 domain revealed by cryo-electron microscopy.bioRxiv : the preprint server for biology · 2025Article
- Solution structure determination and biophysical characterization studies of 7SK RNP and 7SL SRP RNAs.RNA (New York, N.Y.) · 2025Article
- A comprehensive survey and benchmark of deep learning-based methods for atomic model building from cryo-electron microscopy density maps.Briefings in bioinformatics · 2025Article
- Ensemble refinement of mismodeled cryo-EM RNA structures using all-atom simulations.Nature communications · 2025Article
- Cryo-EM reveals remodeling of a tandem riboswitch at 2.9 Å resolution.Research square · 2025Article
- Structural investigation of an RNA device that regulates PD-1 expression in mammalian cells.Nucleic acids research · 2025Article
- Dissemination of pathogenic bacteria is reinforced by a MARTX toxin effector duet.Nature communications · 2024Article
- Gentle and fast all-atom model refinement to cryo-EM densities via a maximum likelihood approach.PLoS computational biology · 2023Article
- Release of frustration drives corneal amyloid disaggregation by brain chaperone.Communications biology · 2023Article
- EMDA: A Python package for Electron Microscopy Data Analysis.Journal of structural biology · 2022Article
- Application of Homology Modeling by Enhanced Profile-Profile Alignment and Flexible-Fitting Simulation to Cryo-EM Based Structure Determination.International journal of molecular sciences · 2022Article
- Unusual nucleosome formation and transcriptome influence by the histone H3mm18 variant.Nucleic acids research · 2022Article
- Integrative structural studies of the SARS-CoV-2 spike protein during the fusion process (2022).Current research in structural biology · 2022Article
- Using cryo-EM to uncover mechanisms of bacterial transcriptional regulation.Biochemical Society transactions · 2021Review
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Cryo-electron microscopy (cryo-EM) is becoming a method of choice for describing native conformations of biomolecular complexes at high resolution. The rapid growth of cryo-EM in recent years has created a high demand for automated solutions, both in hardware and software. Flexible fitting of atomic models to three-dimensional (3D) cryo-EM reconstructions by molecular dynamics (MD) simulation is a popular technique but often requires technical expertise in computer simulation. This work introduces cryo_fit, a package for the automatic flexible fitting of atomic models in cryo-EM maps using MD simulation. The package is integrated with the Phenix software suite. The module was designed to automate the multiple steps of MD simulation in a reproducible manner, as well as facilitate refinement and validation through Phenix. Through the use of cryo_fit, scientists with little experience in MD simulation can produce high quality atomic models automatically and better exploit the potential of cryo-EM.
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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.