Two-Level Approach to Efficient Visualization of Protein Dynamics

Ove Daae Lampe, Ivan Viola, Nathalie Reuter, Helwig Hauser

ARTICLE, IEEE Transactions on Visualization and Computer Graphics (IEEE TVCG), nov, 2007

• paper

Abstract

Proteins are highly flexible and large amplitude deformations of their structure, also called slow dynamics, are often decisive to their function. We present a two-level rendering approach that enables visualization of slow dynamics of large protein assemblies. Our approach is aligned with a hierarchical model of large scale molecules. Instead of constantly updating positions of large amounts of atoms, we update the position and rotation of residues, i.e., higher level building blocks of a protein. Residues are represented by one vertex only indicating its position and additional information defining the rotation. The atoms in the residues are generated on-the-fly on the GPU, exploiting the new graphics hardware geometry shader capabilities. Moreover, we represent the atoms by billboards instead of tessellated spheres. Our representation is then significantly faster and pixel precise. We demonstrate the usefulness of our new approach in the context of our collaborative bioinformatics project.

Published

IEEE Transactions on Visualization and Computer Graphics (IEEE TVCG)

• Volume: 13
• Number: 6
• Pages: 1616–1623
• ISSN: 1077-2626
• Event: IEEE Visualization 2007
• Location: Sacramento, California, USA
• Date: nov 2007

Media

BibTeX

@article{Lampe2007TMV,
  author = {Ove Daae Lampe and Ivan Viola and Nathalie Reuter and Helwig Hauser},
  title = {Two-Level Approach to Efficient Visualization of Protein Dynamics},
  year = {2007},
  month = {nov},
  abstract = {Proteins are highly flexible and large amplitude deformations 
	of their structure, also called slow dynamics, are often decisive to 
	their function. We present a two-level rendering approach that enables 
	visualization of slow dynamics of large protein assemblies. Our approach 
	is aligned with a hierarchical model of large scale molecules. Instead of 
	constantly updating positions of large amounts of atoms, we update the position 
	and rotation of residues, i.e., higher level building blocks of a protein. 
	Residues are represented by one vertex only indicating its position and 
	additional information defining the rotation. The atoms in the residues are 
	generated on-the-fly on the GPU, exploiting the new graphics hardware geometry 
	shader capabilities. Moreover, we represent the atoms by billboards instead of 
	tessellated spheres. Our representation is then significantly faster and pixel 
	precise. We demonstrate the usefulness of our new approach in the context of 
	our collaborative bioinformatics project.},
  journal = {IEEE Transactions on Visualization and Computer Graphics (IEEE TVCG)},
  event = "IEEE Visualization 2007",
  volume = {13},
  number = {6},
  pages = {1616--1623},
  location = "Sacramento, California, USA",

  ISSN = {1077-2626}


}