Visualization and Analysis of Protein Flexibility
Understanding how objects change or move is a challenge across many scientific and engineering
disciplines. As available computational power and working memory increase it is becoming
possible to explore potential changes in more complex systems through simulations at timescales
that were previously thought impossible. Furthermore, simulations that previously were only possible
on supercomputers are now possible on standard desktop equipment. This is especially true
in the fields of structural biology and related disciplines where computational simulations are often
used to predict potential movements or changes of proteins. This dissertation describes tools and
techniques that aim to help researchers more effectively and efficiently understand the results of
these simulations with the help of visualization, analysis and interaction.
The first two of these tools are intended to help researchers more effectively and efficiently
visualize and analyze the results of course grained normal mode analysis. First, I improved static
visualization of protein flexibility by using affine motion models and hierarchical clustering to
model the coordinated motion of groups of residues and draw to arrows showing the direction of
movement of these groups. Second, I used these affine motion models and clustering techniques
to create improved trajectories of the motion of protein molecules. Finally, I developed a novel
system for enabling group discussion and visualization of proteins and their motions on large
stereo displays.
Images and movies
BibTex references
@PhdThesis{Bry11, author = "Bryden, Aaron", title = "Visualization and Analysis of Protein Flexibility", school = "University of Wisconsin Madison", year = "2011", url = "http://graphics.cs.wisc.edu/Papers/2011/Bry11" }