Computational Biophysics Workshop - Pittsburgh, Nov. 28 - Dec. 1, 2005
Lectures
- 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
- 12/1: Simulating
Membrane Channels
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.