MALZAHN, Jan, Barbora KOZLÍKOVÁ a Timo ROPINSKI. Protein Tunnel Reprojection for Physico-Chemical Property Analysis. In S. Bruckner, A. Hennemuth, and B. Kainz. Eurographics Workshop on Visual Computing for Biology and Medicine. Bremen, Germany: Eurographics Workshop on Visual Computing for Biology and Medicine, 2017. s. nestránkováno, 10 s. ISBN 978-3-03868-036-9.
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Základní údaje
Originální název Protein Tunnel Reprojection for Physico-Chemical Property Analysis
Autoři MALZAHN, Jan (276 Německo), Barbora KOZLÍKOVÁ (203 Česká republika, domácí) a Timo ROPINSKI (276 Německo).
Vydání Bremen, Germany, Eurographics Workshop on Visual Computing for Biology and Medicine, od s. nestránkováno, 10 s. 2017.
Nakladatel Eurographics Workshop on Visual Computing for Biology and Medicine
Další údaje
Originální jazyk angličtina
Typ výsledku Stať ve sborníku
Obor 10201 Computer sciences, information science, bioinformatics
Utajení není předmětem státního či obchodního tajemství
Forma vydání elektronická verze "online"
Kód RIV RIV/00216224:14330/17:00097511
Organizační jednotka Fakulta informatiky
ISBN 978-3-03868-036-9
Klíčová slova anglicky Protein;tunnel;projection;visualization
Příznaky Mezinárodní význam, Recenzováno
Změnil Změnila: doc. RNDr. Barbora Kozlíková, Ph.D., učo 60850. Změněno: 26. 4. 2018 12:50.
Anotace
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.
VytisknoutZobrazeno: 19. 3. 2024 03:07