HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures
By Bosco K Ho, Franz Gruswitz. BMC Structural Biology, 2008
436 citations recorded by the source corpus.
BackgroundAn 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.ResultsTo 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.ConclusionThe 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.
Subfields: Atomic and Molecular Physics, and Optics, Biomedical Engineering, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/efe47368c7fc1453ba7b6cd1a6fdfda62acf507f
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Citations in the corpus
- Structural Basis for Allosteric Regulation of GPCRs by Sodium Ions (2012, methodology): “(A) Interior watersin A2AAR-BRIL-ΔC/ZM241385 structure form an almost continuous water channel (grey; calculated using the program Hollow (37)) containing three major water clusters.”
- CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures (2012, background): “Recently, several geometry-based tools for rapid identification and analysis of pathways in protein structures have been developed [35–44].”
- MOLE 2.0: advanced approach for analysis of biomacromolecular channels (2013, methodology): “These methods are used in numerous software tools, such as POCKET [24], LIGSITE [25,26], dxTuber [27], HOLLOW [28], 3V [29], CAVER 1.”