Protein visualization and analysis with VMD

Note

Short URL for this page: https://goo.gl/nGTVXB

This tutorial provides a short introduction to basic use of the VMD (“Visual Molecular Dynamics”) software to visualize and analyze proteins and molecular dynamics trajectories. It is part of the ASU course PHY 542/NAN 542 — Topics in Biophysics I.

For background on using VMD, look at [Hsin2008] and the official VMD tutorial. We will use data from the Protein Databank and [Beckstein2009].

Basics of protein structure are illustrated in [BrandenTooze] and in the lecture notes.

Contents

We are going to work through the individual sections in order. Use the navigation links in menu bar to move forward and backwards.

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

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