ArticlePLoS computational biology2021
Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure.
Article in PLoS computational biology, 2021. 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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19 citing papers in PubMed.
- AFM-Fold: Rapid reconstruction of protein conformations from AFM images.Biophysical journal · 2026Article
- Reconstruction of the Flexible IgM Fc Core Using Atomic Force Microscopy Topography and the AFM-Assembly Pipeline.Journal of molecular recognition : JMR · 2026Article
- Estimating Protein Conformational States from High-Speed AFM Images with Molecular Dynamics and Deep Learning.Journal of chemical information and modeling · 2026Article
- Article
- Deciphering conformational dynamics in AFM data using fast nonlinear NMA and FFT-based search with AFMFit.Communications biology · 2025Article
- A structural biology compatible file format for atomic force microscopy.Nature communications · 2025Article
- CT584 Is Not a Protective Vaccine Antigen against Respiratory Chlamydial Challenge in Mice.Vaccines · 2024Article
- Modeling Conformational Transitions of Biomolecules from Atomic Force Microscopy Images using Normal Mode Analysis.The journal of physical chemistry. B · 2024Article
- Article
- Four Parallel Pathways in T4 Ligase-Catalyzed Repair of Nicked DNA with Diverse Bending Angles.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Evaluation in mice of cell-free produced CT584 as a Chlamydia vaccine antigen.bioRxiv : the preprint server for biology · 2024Article
- Technical advances in high-speed atomic force microscopy.Biophysical reviews · 2023Review
- Simulating biological surface dynamics in high-speed atomic force microscopy experiments.Biophysical reviews · 2023Article
- Spatiotemporal resolution in high-speed atomic force microscopy for studying biological macromolecules in action.Microscopy (Oxford, England) · 2023Review
- BioAFMviewer software for simulation atomic force microscopy of molecular structures and conformational dynamics.Journal of structural biology: X · 2023Review
- Predicting the placement of biomolecular structures on AFM substrates based on electrostatic interactions.Frontiers in molecular biosciences · 2023Article
- Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images.PLoS computational biology · 2022Article
- Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images.PLoS computational biology · 2022Article
- Inferring Conformational State of Myosin Motor in an Atomic Force Microscopy ImageFrontiers in molecular biosciences · 2022Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Atomic force microscopy (AFM) can visualize functional biomolecules near the physiological condition, but the observed data are limited to the surface height of specimens. Since the AFM images highly depend on the probe tip shape, for successful inference of molecular structures from the measurement, the knowledge of the probe shape is required, but is often missing. Here, we developed a method of the rigid-body fitting to AFM images, which simultaneously finds the shape of the probe tip and the placement of the molecular structure via an exhaustive search. First, we examined four similarity scores via twin-experiments for four test proteins, finding that the cosine similarity score generally worked best, whereas the pixel-RMSD and the correlation coefficient were also useful. We then applied the method to two experimental high-speed-AFM images inferring the probe shape and the molecular placement. The results suggest that the appropriate similarity score can differ between target systems. For an actin filament image, the cosine similarity apparently worked best. For an image of the flagellar protein FlhAC, we found the correlation coefficient gave better results. This difference may partly be attributed to the flexibility in the target molecule, ignored in the rigid-body fitting. The inferred tip shape and placement results can be further refined by other methods, such as the flexible fitting molecular dynamics simulations. The developed software is publicly available.
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