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Interactive Exploration of Protein Cavities
Visualization Research Center (VISUS), University of Stuttgart, Germany.
Visualization Research Center (VISUS), University of Stuttgart, Germany.ORCID iD: 0000-0003-1511-5006
Institute for Technical Biochemistry (ITB), University of Stuttgart, Germany.
Institute for Technical Biochemistry (ITB), University of Stuttgart, Germany.
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2011 (English)In: Computer graphics forum (Print), ISSN 0167-7055, E-ISSN 1467-8659, Vol. 30, no 3, p. 673-682Article in journal (Refereed) Published
Abstract [en]

We present a novel application for the interactive exploration of cavities within proteins in dynamic data sets. Inside a protein, cavities can often be found close to the active center. Therefore, when analyzing a molecular dynamics simulation trajectory it is of great interest to find these cavities and determine if such a cavity opens up to the environment, making the binding site accessible to the surrounding substrate. Our user-driven approach enables expert users to select a certain cavity and track its evolution over time. The user is supported by different visualizations of the extracted cavity to facilitate the analysis. The boundary of the protein and its cavities is obtained by means of volume ray casting, where the volume is computed in real-time for each frame, therefore allowing the examination of time-dependent data sets. A fast, partial segmentation of the volume is applied to obtain the selected cavity and trace it over time. Domain experts found our method useful when they applied it exemplarily on two trajectories of lipases from Rhizomucor miehei and Candida antarctica. In both data sets cavities near the active center were easily identified and tracked over time until they reached the surface and formed an open substrate channel.

Place, publisher, year, edition, pages
Blackhorse Publishing, 2011. Vol. 30, no 3, p. 673-682
Keyword [en]
particles, volume
National Category
Media and Communication Technology
Identifiers
URN: urn:nbn:se:liu:diva-143706DOI: 10.1111/j.1467-8659.2011.01916.xOAI: oai:DiVA.org:liu-143706DiVA: diva2:1166256
Available from: 2017-12-14 Created: 2017-12-14 Last updated: 2018-01-13

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CiteExportLink to record
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Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • oxford
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf