Protein Tunnel Reprojection for Physico-Chemical Property Analysis

Kód výsledku v IS VaVaI

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Výsledek na webu

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DOI - Digital Object Identifier

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Jazyk výsledku

angličtina

Název v původním jazyce

Protein Tunnel Reprojection for Physico-Chemical Property Analysis

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

Protein Tunnel Reprojection for Physico-Chemical Property Analysis

Popis výsledku anglicky

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.

Druh

D - Stať ve sborníku

CEP obor

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OECD FORD obor

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Projekt

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Návaznosti

S - Specificky vyzkum na vysokych skolach

Rok uplatnění

2017

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název statě ve sborníku

Eurographics Workshop on Visual Computing for Biology and Medicine

ISBN

9783038680369

ISSN

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e-ISSN

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Počet stran výsledku

10

Strana od-do

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Název nakladatele

Eurographics Workshop on Visual Computing for Biology and Medicine

Místo vydání

Bremen, Germany

Místo konání akce

Bremen

Datum konání akce

1. 1. 2017

Typ akce podle státní příslušnosti

WRD - Celosvětová akce

Kód UT WoS článku

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