HOLLOW: generating accurate representations of channel and interior surfaces in molecular structures

Bosco Ho, Franz Gruswitz

Research output: Contribution to journalArticleResearchpeer-review

282 Citations (Scopus)

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.
Original languageEnglish
Pages (from-to)1 - 6
Number of pages6
JournalBMC Structural Biology
Volume8
DOIs
Publication statusPublished - 2008
Externally publishedYes

Cite this