Two-level approach to efficient visualization of protein dynamics

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

Research output: Contribution to journalArticlepeer-review

38 Scopus citations

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.

Original languageEnglish
Pages (from-to)1616-1623
Number of pages8
JournalIEEE Transactions on Visualization and Computer Graphics
Volume13
Issue number6
StatePublished - 2007
Externally publishedYes
EventIEEE Visualization Conference (Vis 2007)/IEEE Information Visualization Conference (InfoVis 2007) - Sacramento, Canada
Duration: Oct 28 2007Nov 1 2007

Keywords

  • molecular visualization
  • hardware acceleration
  • protein dynamics
  • VIRTUAL ENVIRONMENT
  • MOLECULAR-DYNAMICS
  • NORMAL-MODE

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