title: CHEXVIS: a tool for molecular channel extraction and visualization.
abstract: 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.
  
  
  CONCLUSIONS
  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/ . The web-server is supported on all modern browsers with latest Java plug-in.
authors.affiliation: Department of Computer Science and Automation, Indian Institute of Science, Bangalore, 560012, India. tbmasood@csa.iisc.ernet.in.
authors.forename: Talha Bin
authors.initials: TB
authors.lastname: Masood
authors.affiliation: Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India. sandhya@mbu.iisc.ernet.in.
authors.forename: Sankaran
authors.initials: S
authors.lastname: Sandhya
authors.affiliation: Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India. nchandra@biochem.iisc.ernet.in.
authors.forename: Nagasuma
authors.initials: N
authors.lastname: Chandra
authors.affiliation: Department of Computer Science and Automation, Indian Institute of Science, Bangalore, 560012, India. vijayn@csa.iisc.ernet.in.|Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, 560012, India. vijayn@csa.iisc.ernet.in.
authors.forename: Vijay
authors.initials: V
authors.lastname: Natarajan
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D006801:Humans; D021621:Imaging, Three-Dimensional / Q000379:methods; D007473:Ion Channels / Q000737:chemistry* / Q000302:isolation & purification* / Q000378:metabolism; D008565:Membrane Proteins / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D011487:Protein Conformation; D012984:Software; D055672:Static Electricity; D013379:Substrate Specificity; D014584:User-Computer Interface
chemical_list: D007473:Ion Channels; D008565:Membrane Proteins