Interactive Exploration of Ligand Transportation through Protein Tunnels

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14330%2F17%3A00095871" target="_blank" >RIV/00216224:14330/17:00095871 - isvavai.cz</a>

Result on the web

<a href="http://dx.doi.org/10.1186/s12859-016-1448-0" target="_blank" >http://dx.doi.org/10.1186/s12859-016-1448-0</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1186/s12859-016-1448-0" target="_blank" >10.1186/s12859-016-1448-0</a>

Result language

angličtina

Original language name

Interactive Exploration of Ligand Transportation through Protein Tunnels

Original language description

Background: Protein structures and their interaction with ligands have been in the focus of biochemistry and structural biology research for decades. The transportation of ligand into the protein active site is often complex process, driven by geometric and physico-chemical properties, which renders the ligand path full of jitter and impasses. This prevents understanding of the ligand transportation and reasoning behind its behavior along the path. Results: To address the needs of the domain experts we design an explorative visualization solution based on a multi-scale simplification model. It helps to navigate the user to the most interesting parts of the ligand trajectory by exploring different attributes of the ligand and its movement, such as its distance to the active site, changes of amino acids lining the ligand, or ligand “stuckness”. The process is supported by three linked views – 3D representation of the simplified trajectory, scatterplot matrix, and bar charts with line representation of ligand-lining amino acids. Conclusions: The usage of our tool is demonstrated on molecular dynamics simulations provided by the domain experts. The tool was tested by the domain experts from protein engineering and the results confirm that it helps to navigate the user to the most interesting parts of the ligand trajectory and to understand the ligand behavior.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

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

—

Continuities

S - Specificky vyzkum na vysokych skolach

Publication year

2017

Confidentiality

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

Name of the periodical

BMC Bioinformatics

ISSN

1471-2105

e-ISSN

—

Volume of the periodical

18

Issue of the periodical within the volume

22

Country of publishing house

GB - UNITED KINGDOM

Number of pages

16

Pages from-to

1-16

UT code for WoS article

000397487000002

EID of the result in the Scopus database

2-s2.0-85013756119