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HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures

Bosco K Ho1 and Franz Gruswitz2

Author Affiliations

1 Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco CA 94158-2517, USA

2 Department of Biochemistry and Biophysics, Center for Structure of Membrane Proteins (CSMP), University of California, San Francisco, San Francisco CA 94158-2517, USA

BMC Structural Biology 2008, 8:49  doi:10.1186/1472-6807-8-49

Published: 14 November 2008

Abstract

Background

An accurate rendering of interior surfaces can facilitate the analysis of mechanisms at atomic-level detail, such as the transport of substrates in the ammonia channel. In molecular viewers, one must remove the exterior surface that obscures the channel surface by clipping the viewing plane or manually selecting the channel residues in order to display a partial surface. Neither method is entirely satisfactory, as unwanted additional pieces of surfaces are always generated.

Results

To cleanly visualize a channel surface, we present HOLLOW, a program that generates a "casting" of the interior volume of the protein as dummy atoms. We show that the molecular surface of the dummy atoms closely approximates the channel surface, where this complementary surface of the protein channel can be displayed without superfluous surfaces.

Conclusion

The use of HOLLOW significantly simplifies the generation of channel surfaces, and other interior surfaces of protein structures. HOLLOW is written in PYTHON and is available at http://hollow.sourceforge.net webcite.