J 2020

DockVis: Visual Analysis of Molecular Docking Trajectories

FURMANOVÁ, Katarína, Ondřej VÁVRA, Barbora KOZLÍKOVÁ, Jiří DAMBORSKÝ, Vojtěch VONÁSEK et. al.

Basic information

Original name

DockVis: Visual Analysis of Molecular Docking Trajectories

Authors

FURMANOVÁ, Katarína (703 Slovakia, belonging to the institution), Ondřej VÁVRA (203 Czech Republic, belonging to the institution), Barbora KOZLÍKOVÁ (203 Czech Republic, belonging to the institution), Jiří DAMBORSKÝ (203 Czech Republic, belonging to the institution), Vojtěch VONÁSEK (203 Czech Republic), David BEDNÁŘ (203 Czech Republic, belonging to the institution) and Jan BYŠKA (203 Czech Republic, guarantor, belonging to the institution)

Edition

Computer Graphics Forum, Wiley-Blackwell, 2020, 0167-7055

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10200 1.2 Computer and information sciences

Country of publisher

Switzerland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

Impact factor

Impact factor: 2.078

RIV identification code

RIV/00216224:14330/20:00114201

Organization unit

Faculty of Informatics

DOI

UT WoS

000544268900001

Keywords in English

visual analysis; molecular docking; trajectory; ligand

Tags

International impact, Reviewed
Změněno: 17/2/2023 20:54, Mgr. Michaela Hylsová, Ph.D.

Abstract

V originále

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).

Links

GC18-18647J, research and development project
Name: Vizuální analýza interakcí proteinů a ligandů (Acronym: PROLINT)
Investor: Czech Science Foundation
LM2015047, research and development project
Name: Česká národní infrastruktura pro biologická data (Acronym: ELIXIR-CZ)
Investor: Ministry of Education, Youth and Sports of the CR, Czech National Infrastructure for Biological Data