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Computational Biophysics Workshop - Pittsburgh, Nov. 6-9, 2006

Lectures

• Mon, 11/6: Introduction to Protein Structure and Dynamics
  
  
  • Opening Remarks (pdf) 
  • Molecular Dynamics Method (pdf)
  • Molecular Dynamics of Proteins (pdf)
  • Molecular Dynamics with NAMD (pdf)
  • Molecular Dynamics Analysis - Simulated Cooling (pdf)
     
• Tue, 11/7: Parameters for Classical Force Fields
   
  • Molecular Dynamics Analysis - Temperature Echoes (pdf)
  • Steered Molecular Dynamics (pdf)
  • Force Fields for Molecular Dynamics Simulations (pdf)
     
• Wed, 11/8: Introduction to Bioinformatics
  
  
  • Evolution of Protein Structure (pdf)
  • Sequence and Structure Alignment,  Overview (pdf), Parts I-II (pdf)
  • Evolutionary Studies Using Multiseq in VMD (pdf)
     
• Thu, 11/9: Simulating Membrane Channels
   
  • Transport in Aquaporins (pdf)
  • Nanotubes (pdf)

Suggested Reading:

• "Molecular Modeling: Principles and Applications," by Andrew R. Leach, Longman Press, 1996. Good for beginners.
   
• "Understanding Molecular Simulations: From Algorithms to Applications," by Daan Frenkel and Berend Smit, Academic Press, 1996.
   
• "Computer Simulation of Liquids" by M. P. Allen and D. J., Tildesley, Oxford University Press, 1987. A classic in the field of simulation methods, though it does not specifically deal with macromolecules.
   
• "Molecular Modeling and Simulation" by Tamar Schlick, Springer, 2002.  Good for algorithmic issues.
   
• "Biological Sequence Analysis," by R. Durbin, S. Eddy, A. Krogh, G. Mitchison Cambridge University Press, 1998. A good introduction to sequence alignment methods and bioinformatic methods.
   
• "Introduction to Computational Biology," by M. S. Waterman, Chapman and Hall, 1995. A basic bioinformatic text.