CHEXVIS: a tool for molecular channel extraction and visualization

BMC Bioinformatics

Vijay Natarajan²  Nagasuma Chandra¹  Sankaran Sandhya¹  Talha Bin Masood³ 

[1]Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India

[2]Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560012, India

[3]Department of Computer Science and Automation, Indian Institute of Science, Bangalore 560012, India

关键词: Visualization;    Alpha complex;    Transmembrane pores;    Pores;    Ion channels;    Biomolecular channels;   

Others  :  1177476
DOI  :  10.1186/s12859-015-0545-9

 received in 2014-12-22, accepted in 2015-03-20,  发布年份 2015

【 摘 要 】

Background

Understanding 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.

Results

We 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.

Conclusion

CHEXVIS 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/ webcite. The web-server is supported on all modern browsers with latest Java plug-in.

【 授权许可】

   
2015 Masood et al.; licensee BioMed Central.

【 图 表 】

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