Visual cavity analysis in molecular simulations

Julius Parulek*, Cagatay Turkay, Nathalie Reuter, Ivan Viola

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

20 Scopus citations


Molecular surfaces provide a useful mean for analyzing interactions between biomolecules; such as identification and characterization of ligand binding sites to a host macromolecule. We present a novel technique, which extracts potential binding sites, represented by cavities, and characterize them by 3D graphs and by amino acids. The binding sites are extracted using an implicit function sampling and graph algorithms. We propose an advanced cavity exploration technique based on the graph parameters and associated amino acids. Additionally, we interactively visualize the graphs in the context of the molecular surface. We apply our method to the analysis of MD simulations of Proteinase 3, where we verify the previously described cavities and suggest a new potential cavity to be studied.

Original languageEnglish (US)
Article numberS4
JournalBMC Bioinformatics
StatePublished - 2013
Externally publishedYes

Bibliographical note

Funding Information:
This work has been carried out within the PhysioIllustration research project (# 218023), which is funded by the Norwegian Research Council. A minor part of the project has been funded by the Vienna Science and Technology Fund (WWTF) through project VRG11-010. NR acknowledges funding from the Bergen Research Foundation, and support from the Norwegian Metacenter for Computational Science (NOTUR). We would also like to thank Helwig Hauser and Visualization group in Bergen for useful ideas and feedback. Additionally, we would like to give thanks to anonymous BioVis reviewers for their useful feedback.

Publisher Copyright:
© 2013 Parulek et al.

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics


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