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Computational Biophysics Workshop - Pittsburgh, Jun. 10-14, 2013

• Mon, June 10: Introduction to Protein Structure and Dynamics - Klaus Schulten
  • Welcome and Brief Overview - Ivet Bahar (pdf) (video)
  • Opening Remarks (pdf) (video)
  • Structure and Sequence Analysis with VMD (pdf) (video)
    
  • Introduction to Molecular Dynamics with NAMD (pdf) (video)
    
    
• Tue, June 11: Statistical Mechanics of Protein; Force Field Parameterization - Klaus Schulten and Emad Tajkhorshid
  
• Applications of VMD/NAMD in Modern Research (pdf) (video1, video2)
• Topology, Parameters, and Structure Files (pdf) (video)
  
  
• Wed, June 12: Simulating Membrane Channels - Emad Tajkhorshid
  
  • Introduction and Examples (pdf)
  • Transport in Membrane Channels (pdf) (video)
    


• Thu, June 13: Collective Dynamics of Proteins Using Elastic Network Models - Ivet Bahar, Tim Lezon and Ahmet Bakan
  
  • Elastic Network Models (ENMs) and Collective Motions of Biomolecular Systems using ProDy (pdf) (video1, video2)
  • ProDy Overview and Applications (pdf) (pdf, notebooks) (video)
    
  
  
• Fri, June 14: Druggability Simulations, and Analyzing Sequence Patterns and Structural Dynamics - Ivet Bahar and Ahmet Bakan
  
  • Druggability: Method and Applications (pdf) (video)
  • Comparative Analysis of Sequence Patterns and Structural Dynamics for Families/Ensembles of Proteins (pdf) (video)