BioSpring Examples

Interactive Molecular Simulations of Augmented Elastic Network Models

BioSpring includes a few examples to demonstrate different multi-scale representations and applications. Each example, when accessed through MolPlay, comes with a brief description, detailed documentation, and a video walkthrough. Look for screenshots in our image gallery.

List of Examples

  1. GK BS: interactive enzyme manipulation (coarse-grained)
    • Investigates protein dynamics for an enzyme binding cleft
      • Analysis of conformational changes
      • Investigation of allosteric effects
      • Mechanical properties study
    • Compares with experimental data and more accurate simulations
    • Detailed example walkthrough
  2. OMPT: interactive membrane protein insertion
    • Simulates protein insertion into implicit membrane
      • Implicit membrane representation
      • Support for various membrane geometries
    • Explores preferred orientations and insertion depths
      • Orientation and depth control
      • Real-time parameter monitoring
    • Detailed example walkthrough
  3. Protein-DNA: interactive DNA docking to a protein
    • Demonstrates protein-DNA interactions
      • Interactive positioning
      • Physics-based assembly
    • Explores electrostatic-driven docking
      • Guiding field support
      • Automatic refinement
    • Detailed example walkthrough

Additional Information