BioAFMviewer

BioAFMviewer generates simulated atomic force microscopy (AFM) scans from Protein Data Bank (PDB) structures to visualize biomolecular surface topology and conformational dynamics.

Key Features:

• Simulated Scanning: Performs simulated AFM scans over molecular structures to produce AFM-like graphical outputs.
• Versatile Molecular Viewer: Displays PDB structures with control over orientation for examination from multiple perspectives.
• Variable Spatial Resolution and Tip-Shape Geometry: Allows adjustment of spatial resolution and tip-shape geometry during simulated scanning.
• Dynamic Visualization: Processes molecular movies of protein conformational motions derived from data modeling functional transitions to generate time-resolved simulated AFM frames.

Scientific Applications:

• Comparison with High-Speed AFM Observations: Enables comparison between simulated AFM images and high-speed AFM experimental observations for validation and interpretation.
• Interpretation of Biomolecular Dynamics: Aids interpretation of functional transitions and conformational changes by visualizing dynamic simulations as AFM-like data.

Methodology:

The software reads molecular structures from PDB files and performs synchronized simulated AFM scans with adjustable parameters (spatial resolution, tip geometry) to produce graphical AFM-like outputs for static structures and molecular movies representing conformational transitions.