Elastic Network Models

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Tutorial files: ZIP TGZ

• Introduction
  • Required Programs
  • Recommended Programs
  • Getting Started
• Gaussian Network Model (GNM)
  • Parse structure
  • Build Kirchhoff matrix
  • Parameters
  • Calculate normal modes
  • Normal mode data
  • Individual modes
  • Access hinge sites
  • Plot results
• Anisotropic Network Model (ANM)
  • Parse structure
  • Build Hessian
  • Parameters
  • Calculate normal modes
  • Normal modes data
  • Individual modes
  • Write NMD file
  • View modes in VMD
  • Advanced visualization in jupyter notebooks
• Using an External Matrix
  • Parse Hessian
  • ANM calculations
  • Parse Kirchhoff
  • GNM calculations
• Custom Gamma Functions
  • Parse structure
  • Force Constant Function
  • ANM calculations
• Editing a Model
  • ANM calculations
  • Slicing a model
  • Reducing a model
  • Compare reduced and sliced models
• Extend a coarse-grained model
  • Extrapolation
  • Write NMD file
  • Sample conformers
  • Write PDB file
• Normal Mode Algebra
  • ANM Calculations
  • Calculate overlap
  • Linear combination
  • Approximate a deformation vector
• Deformation Analysis
  • Parse structures
  • Match chains
  • RMSD and superpose
  • Deformation vector
  • Compare with ANM modes

Acknowledgments

Continued development of Protein Dynamics Software ProDy and associated programs is partially supported by the NIH-funded Biomedical Technology and Research Center (BTRC) on High Performance Computing for Multiscale Modeling of Biological Systems (MMBios) (P41 GM103712).