Protein Tunnel Reprojection for Physico-Chemical Property Analysis
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Date
2017
Journal Title
Journal ISSN
Volume Title
Publisher
The Eurographics Association
Abstract
Cavities are crucial for interactions of proteins with other molecules. While a variety of different cavity types exists, tunnels in particular play an important role, as they enable a ligand to deeply enter the active site of a protein where chemical reactions can undergo. Consequently, domain scientists are interested in understanding properties relevant for binding interactions inside molecular tunnels. Unfortunately, when inspecting a 3D representation of the molecule under investigation, tunnels are difficult to analyze due to occlusion issues. Therefore, within this paper we propose a novel reprojection technique that transforms the 3D structure of a molecule to obtain a 2D representation of the tunnel interior. The reprojection has been designed with respect to application-oriented design guidelines, we have identified together with our domain partners. To comply with these guidelines, the transformation preserves individual residues, while the result is capable of showing binding properties inside the tunnel without suffering from occlusions. Thus the reprojected tunnel interior can be used to display physico-chemical properties, e.g., hydrophobicity or amino acid orientation, of residues near a tunnel's surface. As these properties are essential for the interaction between protein and ligand, they can thus hint angles of attack for protein engineers. To demonstrate the benefits of the developed visualization, the obtained results are discussed with respect to domain expert feedback.
Description
@inproceedings{10.2312:vcbm.20171231,
booktitle = {Eurographics Workshop on Visual Computing for Biology and Medicine},
editor = {Stefan Bruckner and Anja Hennemuth and Bernhard Kainz and Ingrid Hotz and Dorit Merhof and Christian Rieder},
title = {{Protein Tunnel Reprojection for Physico-Chemical Property Analysis}},
author = {Malzahn, Jan and Kozlíková, Barbora and Ropinski, Timo},
year = {2017},
publisher = {The Eurographics Association},
ISSN = {2070-5786},
ISBN = {978-3-03868-036-9},
DOI = {10.2312/vcbm.20171231}
}