• Mon, 11/5: Introduction to Protein Structure and Dynamics - E. Tajkhorshid

    • Opening Remarks (pdf)
    • Structure and Sequence Analysis with VMD (pdf)
    • VMD for Structure Building and Dynamics Analysis (pdf)
  • Tue, 11/6: Statistical Mechanics of Proteins - K. Schulten
  • Wed, 11/7: Parameters for Classical Force Fields - E. Tajkhorshid & K. Schulten

    • Molecular Dynamics of Cellular Processes I - E. Tajkhorshid (pdf)
    • Molecular Dynamics of Cellular Processes II - K. Schulten (pdfs: part 1, part 2)

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.