Computational Biophysics Workshop - Frankfurt, Mar. 20-23, 2006

TCB Hands-on Workshop in Frankfurt, Germany

Lectures

3/20: Introduction to Protein Structure and Dynamics
- Opening Remarks (pdf)
- Molecular Graphics Perspective of Protein Structure and Function (pdf)
- Molecular Dynamics Methods (pdf)
3/21: Statistical Mechanics of Proteins
- Equilibrium Properties of Proteins (pdf)
- Using NAMD (pdf)
- Simulated Cooling of Proteins (pdf)
- Temperature Echoes (pdf)
- Steered Molecular Dynamics (pdf)
3/22: Introduction to Bioinformatics
- Evolution of Protein Structure (pdf)
- Sequence and Structure Alignment Algorithms (pdf)
- Bioinformatics of Aquaporins (pdf)
3/23: Simulating Membrane Channels
- Force fields (pdf)
- Transport in Aquaporins (pdf)
- Nanotubes (pdf)

Suggested Reading:

"Scalable molecular dynamics with NAMD," by James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten. Journal of Computational Chemistry, 26:1781-1802, 2005. (Click here for pdf of paper)
"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.