Visual Support for the Loop Grafting Workflow on Proteins

J 2025

Visual Support for the Loop Grafting Workflow on Proteins

OPÁLENÝ, Filip, Pavol ULBRICH, Joan PLANAS IGLESIAS, Jan BYŠKA, Jan ŠTOURAČ et. al.

Basic information

Original name

Visual Support for the Loop Grafting Workflow on Proteins

Authors

OPÁLENÝ, Filip (703 Slovakia, belonging to the institution), Pavol ULBRICH (703 Slovakia, belonging to the institution), Joan PLANAS IGLESIAS (724 Spain, belonging to the institution), Jan BYŠKA (203 Czech Republic, belonging to the institution), Jan ŠTOURAČ (203 Czech Republic, belonging to the institution), David BEDNÁŘ (203 Czech Republic, belonging to the institution), Katarína FURMANOVÁ (703 Slovakia, belonging to the institution) and Barbora KOZLÍKOVÁ (203 Czech Republic, guarantor, belonging to the institution)

Edition

IEEE Transactions on Visualization and Computer Graphics, United States, IEEE Computer Society, 2025, 1077-2626

Other information

Language

English

Type of outcome

Article in a journal

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

United States of America

Confidentiality degree

is not subject to a state or trade secret

References:

URL

Impact factor

Impact factor: 5.200 in 2022

Organization unit

Faculty of Informatics

DOI

http://dx.doi.org/10.1109/TVCG.2024.3456401

UT WoS

999

Keywords in English

Proteins;Visualization;Enzymes;Three Dimensional Displays;Shape;Pipelines;Focusing;Protein Visualization;Protein Engineering;Loop Grafting;Abstract Views

Abstract

V originále

In understanding and redesigning the function of proteins in modern biochemistry, protein engineers are increasingly focusing on exploring regions in proteins called loops. Analyzing various characteristics of these regions helps the experts design the transfer of the desired function from one protein to another. This process is denoted as loop grafting. We designed a set of interactive visualizations that provide experts with visual support through all the loop grafting pipeline steps. The workflow is divided into several phases, reflecting the steps of the pipeline. Each phase is supported by a specific set of abstracted 2D visual representations of proteins and their loops that are interactively linked with the 3D View of proteins. By sequentially passing through the individual phases, the user shapes the list of loops that are potential candidates for loop grafting. Finally, the actual in-silico insertion of the loop candidates from one protein to the other is performed, and the results are visually presented to the user. In this way, the fully computational rational design of proteins and their loops results in newly designed protein structures that can be further assembled and tested through in-vitro experiments. We showcase the contribution of our visual support design on a real case scenario changing the enantiomer selectivity of the engineered enzyme. Moreover, we provide the readers with the experts' feedback.

Links

MUNI/A/1590/2023, interní kód MU

Name: Využití technik umělé inteligence pro zpracování dat, komplexní analýzy a vizualizaci rozsáhlých dat

Investor: Masaryk University, Using artificial intelligence techniques for data processing, complex analysis and visualization of large-scale data

MUNI/A/1608/2023, interní kód MU

Name: Zapojení studentů Fakulty informatiky do mezinárodní vědecké komunity 24

Investor: Masaryk University

Citovat

OPÁLENÝ, Filip, Pavol ULBRICH, Joan PLANAS IGLESIAS, Jan BYŠKA, Jan ŠTOURAČ, David BEDNÁŘ, Katarína FURMANOVÁ and Barbora KOZLÍKOVÁ. Visual Support for the Loop Grafting Workflow on Proteins. IEEE Transactions on Visualization and Computer Graphics. United States: IEEE Computer Society, 2025, vol. 31, No 1, p. 580-590. ISSN 1077-2626. Available from: https://dx.doi.org/10.1109/TVCG.2024.3456401.

@article{2419834,
   author = {Opálený, Filip and Ulbrich, Pavol and Planas Iglesias, Joan and Byška, Jan and Štourač, Jan and Bednář, David and Furmanová, Katarína and Kozlíková, Barbora},
   article_location = {United States},
   article_number = {1},
   doi = {http://dx.doi.org/10.1109/TVCG.2024.3456401},
   keywords = {Proteins;Visualization;Enzymes;Three Dimensional Displays;Shape;Pipelines;Focusing;Protein Visualization;Protein Engineering;Loop Grafting;Abstract Views},
   language = {eng},
   issn = {1077-2626},
   journal = {IEEE Transactions on Visualization and Computer Graphics},
   title = {Visual Support for the Loop Grafting Workflow on Proteins},
   url = {https://www.computer.org/csdl/journal/tg/2025/01/10670529/207JN7FTyfu},
   volume = {31},
   year = {2025}
}

TY  - JOUR
ID  - 2419834
AU  - Opálený, Filip - Ulbrich, Pavol - Planas Iglesias, Joan - Byška, Jan - Štourač, Jan - Bednář, David - Furmanová, Katarína - Kozlíková, Barbora
PY  - 2025
TI  - Visual Support for the Loop Grafting Workflow on Proteins
JF  - IEEE Transactions on Visualization and Computer Graphics
VL  - 31
IS  - 1
SP  - 580-590
EP  - 580-590
PB  - IEEE Computer Society
SN  - 10772626
KW  - Proteins;Visualization;Enzymes;Three Dimensional Displays;Shape;Pipelines;Focusing;Protein Visualization;Protein Engineering;Loop Grafting;Abstract Views
UR  - https://www.computer.org/csdl/journal/tg/2025/01/10670529/207JN7FTyfu
N2  - In understanding and redesigning the function of proteins in modern biochemistry, protein engineers are increasingly focusing on exploring regions in proteins called loops. Analyzing various characteristics of these regions helps the experts design the transfer of the desired function from one protein to another. This process is denoted as loop grafting. We designed a set of interactive visualizations that provide experts with visual support through all the loop grafting pipeline steps. The workflow is divided into several phases, reflecting the steps of the pipeline. Each phase is supported by a specific set of abstracted 2D visual representations of proteins and their loops that are interactively linked with the 3D View of proteins. By sequentially passing through the individual phases, the user shapes the list of loops that are potential candidates for loop grafting. Finally, the actual in-silico insertion of the loop candidates from one protein to the other is performed, and the results are visually presented to the user. In this way, the fully computational rational design of proteins and their loops results in newly designed protein structures that can be further assembled and tested through in-vitro experiments. We showcase the contribution of our visual support design on a real case scenario changing the enantiomer selectivity of the engineered enzyme. Moreover, we provide the readers with the experts' feedback.
ER  -

OPÁLENÝ, Filip, Pavol ULBRICH, Joan PLANAS IGLESIAS, Jan BYŠKA, Jan ŠTOURAČ, David BEDNÁŘ, Katarína FURMANOVÁ and Barbora KOZLÍKOVÁ. Visual Support for the Loop Grafting Workflow on Proteins. \textit{IEEE Transactions on Visualization and Computer Graphics}. United States: IEEE Computer Society, 2025, vol.~31, No~1, p.~580-590. ISSN~1077-2626. Available from: https://dx.doi.org/10.1109/TVCG.2024.3456401.

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