ArticlePLoS computational biology2022
Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images.
Article in PLoS computational biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed, 58 citations in OpenAlex.
- High-speed atomic force microscopy of membrane proteins: From dynamic imaging to integrative structural biology.Current opinion in structural biology · 2026Review
- AFM-Fold: Rapid reconstruction of protein conformations from AFM images.Biophysical journal · 2026Article
- Article
- Multivalent Interactions between Chaperone and Ribosome-Nascent Chain Complex Revealed by High-Speed AFM and MD Simulations.ACS nano · 2025Article
- Article
- Deciphering conformational dynamics in AFM data using fast nonlinear NMA and FFT-based search with AFMFit.Communications biology · 2025Article
- Structural insights into heterohexameric assembly of epilepsy-related ligand-receptor complex LGI1-ADAM22.eLife · 2025Article
- Modulation of SARS-CoV-2 spike binding to ACE2 through conformational selection.Nature nanotechnology · 2025Article
- A structural biology compatible file format for atomic force microscopy.Nature communications · 2025Article
- Nano-Scale Video Imaging of Motility Machinery by High-Speed Atomic Force Microscopy.Biomolecules · 2025Review
- Modeling Conformational Transitions of Biomolecules from Atomic Force Microscopy Images using Normal Mode Analysis.The journal of physical chemistry. B · 2024Article
- Article
- Real-Time Multistep Asymmetrical Disassembly of Nucleosomes and Chromatosomes Visualized by High-Speed Atomic Force Microscopy.ACS central science · 2024Article
- Structural heterogeneity of the ion and lipid channel TMEM16F.Nature communications · 2024Article
- Structural Dynamics of E6AP E3 Ligase HECT Domain and Involvement of a Flexible Hinge Loop in the Ubiquitin Chain Synthesis Mechanism.Nano letters · 2023Article
- High-speed atomic force microscopy: extracting high-resolution information through image analysis.Biophysical reviews · 2023Article
- Simulating biological surface dynamics in high-speed atomic force microscopy experiments.Biophysical reviews · 2023Article
- Characteristics and Functionality of Cantilevers and Scanners in Atomic Force Microscopy.Materials (Basel, Switzerland) · 2023Review
- Single-molecule imaging of genome maintenance proteins encountering specific DNA sequences and structures.DNA repair · 2023Review
- Spatiotemporal resolution in high-speed atomic force microscopy for studying biological macromolecules in action.Microscopy (Oxford, England) · 2023Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Atomic force microscopy (AFM) can visualize the dynamics of single biomolecules under near-physiological conditions. However, the scanning tip probes only the molecular surface with limited resolution, missing details required to fully deduce functional mechanisms from imaging alone. To overcome such drawbacks, we developed a computational framework to reconstruct 3D atomistic structures from AFM surface scans, employing simulation AFM and automatized fitting to experimental images. We provide applications to AFM images ranging from single molecular machines, protein filaments, to large-scale assemblies of 2D protein lattices, and demonstrate how the obtained full atomistic information advances the molecular understanding beyond the original topographic AFM image. We show that simulation AFM further allows for quantitative molecular feature assignment within measured AFM topographies. Implementation of the developed methods into the versatile interactive interface of the BioAFMviewer software, freely available at www.bioafmviewer.com, presents the opportunity for the broad Bio-AFM community to employ the enormous amount of existing structural and modeling data to facilitate the interpretation of resolution-limited AFM images.
Indexed as
Identifiers
What OpenQuestion holds
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.