ArticlePLoS computational biology2020
BioAFMviewer: An interactive interface for simulated AFM scanning of biomolecular structures and dynamics.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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47 citing papers in PubMed, 90 citations in OpenAlex.
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- Real-time visualization of spatial and temporal coordination in resolvase-mediated Holliday junction binding.iScience · 2026Article
- Structural Dynamics of the Afamin/Wnt3a Complex Mediated by the Afamin Hydrophobic Pocket.Nano letters · 2026Article
- Estimating Protein Conformational States from High-Speed AFM Images with Molecular Dynamics and Deep Learning.Journal of chemical information and modeling · 2026Article
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- Multivalent Interactions between Chaperone and Ribosome-Nascent Chain Complex Revealed by High-Speed AFM and MD Simulations.ACS nano · 2025Article
- Automated registration and clustering for enhanced localization atomic force microscopy of flexible membrane proteins.PLoS computational biology · 2025Article
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- Structural insights into heterohexameric assembly of epilepsy-related ligand-receptor complex LGI1-ADAM22.eLife · 2025Article
- Zooming into Gene Activation: Estrogen Receptor α Dimerization and DNA Binding Visualized by High-Speed Atomic Force Microscopy.ACS nano · 2025Article
- Nanoscopic Profiling of Small Extracellular Vesicles via High-Speed Atomic Force Microscopy (HS-AFM) Videography.Journal of extracellular vesicles · 2025Article
- Modeling Conformational Transitions of Biomolecules from Atomic Force Microscopy Images using Normal Mode Analysis.The journal of physical chemistry. B · 2024Article
- Multi-view neural 3D reconstruction of micro- and nanostructures with atomic force microscopy.Communications engineering · 2024Article
- Molecular-Scale Investigations Reveal the Effect of Natural Polyphenols on BAX/Bcl-2 Interactions.International journal of molecular sciences · 2024Article
- Observing Dynamic Conformational Changes within the Coiled-Coil Domain of Different Laminin Isoforms Using High-Speed Atomic Force Microscopy.International journal of molecular sciences · 2024Article
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We provide a stand-alone software, the BioAFMviewer, which transforms biomolecular structures into the graphical representation corresponding to the outcome of atomic force microscopy (AFM) experiments. The AFM graphics is obtained by performing simulated scanning over the molecular structure encoded in the corresponding PDB file. A versatile molecular viewer integrates the visualization of PDB structures and control over their orientation, while synchronized simulated scanning with variable spatial resolution and tip-shape geometry produces the corresponding AFM graphics. We demonstrate the applicability of the BioAFMviewer by comparing simulated AFM graphics to high-speed AFM observations of proteins. The software can furthermore process molecular movies of conformational motions, e.g. those obtained from servers which model functional transitions within a protein, and produce the corresponding simulated AFM movie. The BioAFMviewer software provides the platform to employ the plethora of structural and dynamical data of proteins in order to help in the interpretation of biomolecular AFM experiments.
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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.