Computational Biophysics Workshop - Boston, Dec. 5-9, 2004
Lectures
- 12/5: Introduction to Protein Structure and Dynamics
- 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
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.
