Protein Tunnel Reprojection for Physico-Chemical Property Analysis

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14330%2F17%3A00097511" target="_blank" >RIV/00216224:14330/17:00097511 - isvavai.cz</a>

Result on the web

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DOI - Digital Object Identifier

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Result language

angličtina

Original language name

Protein Tunnel Reprojection for Physico-Chemical Property Analysis

Original language description

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.

Czech name

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Czech description

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Type

D - Article in proceedings

CEP classification

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OECD FORD branch

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

Project

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Continuities

S - Specificky vyzkum na vysokych skolach

Publication year

2017

Confidentiality

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

Article name in the collection

Eurographics Workshop on Visual Computing for Biology and Medicine

ISBN

9783038680369

ISSN

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e-ISSN

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Number of pages

10

Pages from-to

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Publisher name

Eurographics Workshop on Visual Computing for Biology and Medicine

Place of publication

Bremen, Germany

Event location

Bremen

Event date

Jan 1, 2017

Type of event by nationality

WRD - Celosvětová akce

UT code for WoS article

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