DockVis: Visual Analysis of Molecular Docking Trajectories

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14330%2F20%3A00114201" target="_blank" >RIV/00216224:14330/20:00114201 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/68407700:21230/20:00342316 RIV/00159816:_____/20:00073450

Výsledek na webu

<a href="http://onlinelibrary.wiley.com/doi/10.1111/cgf.14048" target="_blank" >http://onlinelibrary.wiley.com/doi/10.1111/cgf.14048</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1111/cgf.14048" target="_blank" >10.1111/cgf.14048</a>

Jazyk výsledku

angličtina

Název v původním jazyce

DockVis: Visual Analysis of Molecular Docking Trajectories

Popis výsledku v původním jazyce

Computation of trajectories for ligand binding and unbinding via protein tunnels and channels is important for predicting possible protein-ligand interactions. These highly complex processes can be simulated by several software tools, which provide biochemists with valuable information for drug design or protein engineering applications. This paper focuses on aiding this exploration process by introducing the DockVis visual analysis tool. DockVis operates with the multivariate output data from one of the latest available tools for the prediction of ligand transport, CaverDock. DockVis provides the users with several linked views, combining the 2D abstracted depictions of ligands and their surroundings and properties with the 3D view. In this way,we enable the users to perceive the spatial configurations of ligand passing through the protein tunnel. The users are initially visually directed to the most relevant parts of ligand trajectories, which can be then explored in higher detail by the follow-up analyses. DockVis was designed in tight collaboration with protein engineers developing the CaverDock tool. However, the concept of DockVis can be extended to any other tool predicting ligand pathways by the molecular docking. DockVis will be made available to the wide user community as part of the Caver Analyst 3.0 software package (www.caver.cz).

Název v anglickém jazyce

DockVis: Visual Analysis of Molecular Docking Trajectories

Popis výsledku anglicky

Computation of trajectories for ligand binding and unbinding via protein tunnels and channels is important for predicting possible protein-ligand interactions. These highly complex processes can be simulated by several software tools, which provide biochemists with valuable information for drug design or protein engineering applications. This paper focuses on aiding this exploration process by introducing the DockVis visual analysis tool. DockVis operates with the multivariate output data from one of the latest available tools for the prediction of ligand transport, CaverDock. DockVis provides the users with several linked views, combining the 2D abstracted depictions of ligands and their surroundings and properties with the 3D view. In this way,we enable the users to perceive the spatial configurations of ligand passing through the protein tunnel. The users are initially visually directed to the most relevant parts of ligand trajectories, which can be then explored in higher detail by the follow-up analyses. DockVis was designed in tight collaboration with protein engineers developing the CaverDock tool. However, the concept of DockVis can be extended to any other tool predicting ligand pathways by the molecular docking. DockVis will be made available to the wide user community as part of the Caver Analyst 3.0 software package (www.caver.cz).

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10200 - Computer and information sciences

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>S - Specificky vyzkum na vysokych skolach<br>I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2020

Kód důvěrnosti údajů

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

Název periodika

Computer Graphics Forum

ISSN

0167-7055

e-ISSN

1467-8659

Svazek periodika

39

Číslo periodika v rámci svazku

6

Stát vydavatele periodika

CH - Švýcarská konfederace

Počet stran výsledku

13

Strana od-do

452-464

Kód UT WoS článku

000544268900001

EID výsledku v databázi Scopus

2-s2.0-85087214556