Importance Driven Visualization of Molecular Surfaces

Julius Parulek, Timo Ropinski, Ivan Viola
Importance Driven Visualization of Molecular Surfaces
Poster shown at 3rd IEEE Symposium on Biological Data Visualization (2013-10-13-2013-10-14) In . October 2013.
[Poster]

Information

Abstract

We present a novel rendering method, based on the level-of-detail concept, which shows protein complexes over time in real-time. We exploit three different molecular surface models, solvent excluded surface (SES), Gaussian kernels and van der Waals spheres combined in one seamless visualization. As a general rule, closest to the viewer we aim at providing a maximum of relevant information related to the structure and binding sites. Such information is conveyed by the SES representation. Farther away from the viewer, we are smoothly changing the visual representation to an approximation of SES through Gaussian kernels. The least detailed representation is based on simple sphere splatting and is dedicated to structures farthest away from the viewer. A more general solution leads us to the definition of a 3D importance function that is based on the distance measure from a molecular feature. In order to preserve smoothness in transition areas, we introduce three shading levels that correspond to their geometric counterparts and a method for creating seamless transition between these representations. The SES representation with full shading and added contours stands in focus while on the other side a sphere representation with constant shading and without contours provide the context. Moreover, we introduce a methodology to render the entire molecule directly using the A-buffer technique, which further improves the performance. The rendering performance is evaluated on series of molecules of varying atom counts.

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BibTeX

@misc{Viola_2013_IDV,
  title =      "Importance Driven Visualization of Molecular Surfaces",
  author =     "Julius Parulek and Timo Ropinski and Ivan Viola",
  year =       "2013",
  abstract =   "We present a novel rendering method, based on the
               level-of-detail concept, which shows protein complexes over
               time in real-time. We exploit three different molecular
               surface models, solvent excluded surface (SES), Gaussian
               kernels and van der Waals spheres combined in one seamless
               visualization. As a general rule, closest to the viewer we
               aim at providing a maximum of relevant information related
               to the structure and binding sites. Such information is
               conveyed by the SES representation. Farther away from the
               viewer, we are smoothly changing the visual representation
               to an approximation of SES through Gaussian kernels. The
               least detailed representation is based on simple sphere
               splatting and is dedicated to structures farthest away from
               the viewer. A more general solution leads us to the
               definition of a 3D importance function that is based on the
               distance measure from a molecular feature. In order to
               preserve smoothness in transition areas, we introduce three
               shading levels that correspond to their geometric
               counterparts and a method for creating seamless transition
               between these representations. The SES representation with
               full shading and added contours stands in focus while on the
               other side a sphere representation with constant shading and
               without contours provide the context. Moreover, we introduce
               a methodology to render the entire molecule directly using
               the A-buffer technique, which further improves the
               performance. The rendering performance is evaluated on
               series of molecules of varying atom counts.",
  month =      oct,
  event =      "3rd IEEE Symposium on Biological Data Visualization",
  location =   "Atlanta, GA",
  publisher =  "BioVis website (http://www.biovis.net/year/2013/posters)",
  note =       "Poster presented at 3rd IEEE Symposium on Biological Data
               Visualization (2013-10-13--2013-10-14)",
  pages =      "--",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2013/Viola_2013_IDV/",
}