TCB Hands-on Workshop in San Francisco


  • 11/28: Introduction to Protein Structure and Dynamics

    • Molecular Graphics Perspective of Protein Structure and Function
    • Molecular Dynamics Method
  • 11/29: Statistical Mechanics of Proteins
    • Equilibrium Properties of Proteins
    • Using NAMD
    • Simulated Cooling of Proteins
    • Temperature Echoes
  • 11/30: Parameters of Classical Force Fields
    • Introduction and Examples (pdf)
    • Introduction to Classical Force Fields (pdf)
    • Methods of Parameterization (pdf)
  • 12/1: 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.