Protein Tunnel Reprojection for Physico-Chemical Property Analysis (Unknown language)

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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.

Table of contents conference proceedings

The tables of contents are generated automatically and are based on the data records of the individual contributions available in the index of the TIB portal. The display of the Tables of Contents may therefore be incomplete.

1
Protein Tunnel Reprojection for Physico-Chemical Property Analysis
Malzahn, Jan / Kozlíková, Barbora / Ropinski, Timo | 2017
11
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21
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27
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33
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Vad, Viktor / Byška, Jan / Jurcík, Adam / Viola, Ivan / Gröller, Eduard / Hauser, Helwig / Margues, Sérgio M. / Damborský, Jiří / Kozlíková, Barbora | 2017
43
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53
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Zhang, Changgong / Höllt, Thomas / Caan, Matthan W. A. / Eisemann, Elmar / Vilanova, Anna | 2017
63
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Ji, Chengtao / Gronde, Jasper J. van de / Maurits, Natasha M. / Roerdink, Jos B. T. M. | 2017
73
HIFUtk: Visual Analytics for High Intensity Focused Ultrasound Simulation
Modena, Daniela / Dijk, Edmond van / Bošnacki, Dragan / Eikelder, Huub M. M. ten / Westenberg, Michel A. | 2017
83
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Alpers, Julian / Hansen, Christian / Ringe, Kristina / Rieder, Christian | 2017
93
Visual Navigation Support for Liver Applicator Placement using Interactive Map Displays
Hettig, Julian / Mistelbauer, Gabriel / Rieder, Christian / Lawonn, Kai / Hansen, Christian | 2017
103
Application of Image Processing Functions for Brain Tumor Enhancement in Intraoperative Ultrasound Image Data
Chalopin, Claire / Mbuyamba, Elisee Ilunga / Aragon, Jesus Guillermo Cabal / Rodriguez, Juan Carlos Camacho / Arlt, Felix / Cervantes, Juan Gabriel Avina / Meixensberger, Juergen / Lindner, Dirk | 2017
113
MRI Hip Joint Segmentation: A Locally Bhattacharyya Weighted Hybrid 3D Level Set Approach
Pham, Duc Duy / Morariu, Cosmin Adrian / Terheiden, Tobias / Landgraeber, Stefan / Jäger, Marcus / Pauli, Josef | 2017
119
Multi-fiber Estimation and Tractography for Diffusion MRI using mixture of Non-central Wishart Distributions
Shakya, Snehlata / Gu, Xuan / Batool, Nazre / Özarslan, Evren / Knutsson, Hans | 2017
125
Automatic Thrombus Detection in Non-enhanced Computed Tomography Images in Patients With Acute Ischemic Stroke
Löber, Patrick / Stimpel, Bernhard / Syben, Christopher / Maier, Andreas / Ditt, Hendrik / Schramm, Peter / Raczkowski, Boy / Kemmling, André | 2017
131
Maximizing AUC with Deep Learning for Classification of Imbalanced Mammogram Datasets
Sulam, Jeremias / Ben-Ari, Rami / Kisilev, Pavel | 2017
137
A Web-Based Tool for Cardiac Dyssynchrony Assessment on Ultrasound Data
Pezzatini, Daniele / Yagüe, Carlos / Rudenick, Paula / Blat, Josep / Bijnens, Bart / Camara, Oscar | 2017
143
UI-Net: Interactive Artificial Neural Networks for Iterative Image Segmentation Based on a User Model
Amrehn, Mario / Gaube, Sven / Unberath, Mathias / Schebesch, Frank / Horz, Tim / Strumia, Maddalena / Steidl, Stefan / Kowarschik, Markus / Maier, Andreas | 2017
149
Bone Fracture and Lesion Assessment using Shape-Adaptive Unfolding
Martinke, Hannes / Petry, Christian / Großkopf, Stefan / Suehling, Michael / Soza, Grzegorz / Preim, Bernhard / Mistelbauer, Gabriel | 2017
159
Combining Pseudo Chroma Depth Enhancement and Parameter Mapping for Vascular Surface Models
Behrendt, Benjamin / Berg, Philipp / Preim, Bernhard / Saalfeld, Sylvia | 2017
169
Exploration of Interventricular Septum Motion in Multi-Cycle Cardiac MRI
Tautz, Lennart / Hüllebrand, Markus / Steinmetz, Michael / Voit, Dirk / Frahm, Jens / Hennemuth, Anja | 2017
179
Concentric Circle Glyphs for Enhanced Depth-Judgment in Vascular Models
Lichtenberg, Nils / Hansen, Christian / Lawonn, Kai | 2017
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