ArticleNature communications2025
A structural biology compatible file format for atomic force microscopy.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- High-speed atomic force microscopy of membrane proteins: From dynamic imaging to integrative structural biology.Current opinion in structural biology · 2026Review
- Automating Model Building for SPM Images of Biomolecules Using MISO.Journal of chemical information and modeling · 2026Article
- Self-supervised image denoising and restoration method for atomic force microscopy.Nature communications · 2026Article
- From possibility to precision in macromolecular ensemble prediction.Nature methods · 2026Article
- SimHS-AFMfit-MD: An Integrative Approach for Inferring Alpha-Actinin Atomic Conformational Dynamics.Nano letters · 2026Article
- Zooming into Gene Activation: Estrogen Receptor α Dimerization and DNA Binding Visualized by High-Speed Atomic Force Microscopy.ACS nano · 2025Article
- A structural biology compatible file format for atomic force microscopy.Nature communications · 2025Article
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Authors and funding
3 authors.
Funding
Abstract
Cryogenic electron microscopy (cryo-EM), X-ray crystallography, and nuclear magnetic resonance (NMR) contribute structural data that are interchangeable, cross-verifiable, and visualizable on common platforms, making them powerful tools for our understanding of protein structures. Unfortunately, atomic force microscopy (AFM) has so far failed to interface with these structural biology methods, despite the recent development of localization AFM (LAFM) that allows extracting high-resolution structural information from AFM data. Here, we build on LAFM and develop a pipeline that transforms AFM data into 3D-density files (.afm) that are readable by programs commonly used to visualize, analyze, and interpret structural data. We show that 3D-LAFM densities can serve as force fields to steer molecular dynamics flexible fitting (MDFF) to obtain structural models of previously unresolved states based on AFM observations in close-to-native environment. Besides, the .afm format enables direct 3D or 2D visualization and analysis of conventional AFM images. We anticipate that the file format will find wide usage and embed AFM in the repertoire of methods routinely used by the structural biology community, allowing AFM researchers to deposit data in repositories in a format that allows comparison and cross-verification with data from other techniques.
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Registered trials
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