TCB Hands-on Workshop in Boston

Lectures

  • 12/5: Introduction to Protein Structure and Dynamics 
    • Opening Remarks(pdf
    • Molecular Graphics Perspective of Protein Structure and Function(pdf)
    • Molecular Dynamics Methods (pdf)

  • 12/6: Statistical Mechanics of Proteins
    • Equilibrium Properties of Proteins (pdf
    • Simulated Cooling of Proteins (pdf)
    • Temperature Echoes (pdf)
    • Examples of Steered Molecular Dynamics (pdf)
    • Using NAMD (pdf

  • 12/7: Introduction to Bioinformatics ;
    • Sequence and Structure Alignment Algorithms (pdf
    • Evolution of Protein Structure (pdf)
    • Bioinformatics of Aquaporins (pdf

  • 12/8: Parameters of Classical Force Fields
    • Introduction and Examples
    • Introduction to Classical Force Fields (pdf)
    • Methods of Parametrization (pdf)

  • 12/9: Simulating Membrane Channels
    • Introduction and Examples (pdf)
    • 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.