MolPlay Examples

Interactive Molecular Simulations and Analyses Examples

MolPlay includes a variety of examples to demonstrate different IMSA techniques and applications. Each example comes with a brief description, detailed documentation, and a video walkthrough.

List of Examples

  1. BPTI: interactive protein simulation
    • Demonstrates protein dynamics in water
    • Explores force propagation and structural manipulation
  2. Deca-alanine helix in water: interactive peptide simulation
    • Simple system for beginners
    • Demonstrates basic molecular dynamics
  3. DMPC: interactive membrane simulation
    • Explores lipid bilayer dynamics
    • Demonstrates membrane perturbation and lipid extraction
  4. GK BS: interactive enzyme manipulation (coarse-grained)
    • Investigates enzyme binding cleft dynamics
    • Compares with all-atom simulation
  5. GK: interactive enzyme simulation (all-atom)
    • Explores allosteric effects in enzymes
    • Allows comparison with coarse-grained model
  6. OMPT: interactive membrane protein insertion
    • Simulates protein insertion into implicit membrane
    • Explores preferred orientations and insertion depths
  7. Protein-DNA: interactive DNA docking to a protein
    • Demonstrates protein-DNA interactions
    • Explores electrostatic-driven docking
  8. SNARE complex: interactive double membrane protein bundle simulation
    • Investigates mechanical properties of membrane fusion proteins
    • Demonstrates force propagation analysis
  9. VAMP-CG-v1: interactive membrane peptide simulation
    • Small coarse-grained bilayer system
    • Explores membrane - protein - water - ion interactions

Additional Information