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CHEXVIS: a tool for molecular channel extraction and visualization

Authors
  • Masood, Talha Bin1
  • Sandhya, Sankaran2
  • Chandra, Nagasuma2
  • Natarajan, Vijay1, 3
  • 1 Indian Institute of Science, Department of Computer Science and Automation, Bangalore, 560012, India , Bangalore (India)
  • 2 Indian Institute of Science, Department of Biochemistry, Bangalore, 560012, India , Bangalore (India)
  • 3 Indian Institute of Science, Supercomputer Education and Research Centre, Bangalore, 560012, India , Bangalore (India)
Type
Published Article
Journal
BMC Bioinformatics
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Apr 16, 2015
Volume
16
Issue
1
Identifiers
DOI: 10.1186/s12859-015-0545-9
Source
Springer Nature
Keywords
License
Green

Abstract

BackgroundUnderstanding channel structures that lead to active sites or traverse the molecule is important in the study of molecular functions such as ion, ligand, and small molecule transport. Efficient methods for extracting, storing, and analyzing protein channels are required to support such studies. Further, there is a need for an integrated framework that supports computation of the channels, interactive exploration of their structure, and detailed visual analysis of their properties.ResultsWe describe a method for molecular channel extraction based on the alpha complex representation. The method computes geometrically feasible channels, stores both the volume occupied by the channel and its centerline in a unified representation, and reports significant channels. The representation also supports efficient computation of channel profiles that help understand channel properties. We describe methods for effective visualization of the channels and their profiles. These methods and the visual analysis framework are implemented in a software tool, ChExVis. We apply the method on a number of known channel containing proteins to extract pore features. Results from these experiments on several proteins show that ChExVis performance is comparable to, and in some cases, better than existing channel extraction techniques. Using several case studies, we demonstrate how ChExVis can be used to study channels, extract their properties and gain insights into molecular function.ConclusionChExVis supports the visual exploration of multiple channels together with their geometric and physico-chemical properties thereby enabling the understanding of the basic biology of transport through protein channels. The ChExVis web-server is freely available at http://vgl.serc.iisc.ernet.in/chexvis/. The web-server is supported on all modern browsers with latest Java plug-in.

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