Practical 10: Protein dynamics and visualization

For background on using VMD, look at [Hsin2008] and the VMD tutorial.

Basics of protein structure are illustrated in [BrandenTooze].

Contents:

• Basics of protein structure
• Analyzing protein structure and topology
• Publication-quality images
• Analyzing protein dynamics
• Making movies in VMD

Learning Objectives

• basic understanding of protein structure
• familiarize with a molecular graphics program (VMD)
• loading of static structures and dynamics trajectories
• viewing a molecule (mouse, view modes)
• representations
• selections
• making images
• basic analysis
• use of RMSFitting tools

References

[BrandenTooze]

C. Branden and J. Tooze. Introduction to Protein Structure. 2nd ed, 1999, Garland Publishing, New York.

[Hsin2008]

J. Hsin, A. Arkhipov, Y. Yin, J. E. Stone, and K. Schulten. Using VMD: An Introductory Tutorial, volume 24, chapter 5.7, pages 5.7.1–5.7.48. John Wiley & Sons, Inc., 2008. URL http://dx.doi.org/10.1002/0471250953.bi0507s24.

[Beckstein2009]

O Beckstein. EJ Denning, JR Perilla, and TB Woolf. Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open/Closed Transitions. J Mol Biol 394 (2009), 160–176. http://dx.doi.org/10.1016/j.jmb.2009.09.009

Indices and tables

• Index
• Module Index
• Search Page