Computational Biophysics Workshop - Chicago, Jun. 9-13, 2005

TCB Hands-on Workshop in Chicago

Lectures

  • 6/9: Introduction to Protein Structure and Dynamics

    • Opening Remarks (pdf) 
    • Welcome from the TCB Group (pdf)
    • Molecular Graphics Perspective of Protein Structure and Function (pdf)
    • Molecular Dynamics Methods (pdf)
       
  • 6/10: Introduction to Bioinformatics

    • Evolution of Protein Structure (pdf)
    • Sequence and Structure Alignment Algorithms (pdf)
    • Bioinformatics of Aquaporins (pdf)
       
  • 6/11: Statistical Mechanics of Proteins
     
    • Equilibrium Properties of Proteins (pdf)
    • Using NAMD (pdf)
    • Simulated Cooling of Proteins (pdf)
    • Temperature Echoes (pdf)
     
  • 6/12: Parameters of Classical Force Fields
     
    • Introduction and Examples (pdf)
    • Introduction to Classical Force Fields (pdf)
    • Methods of Parameterization (pdf)
       
  • 6/13: 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.