Visual Analysis of Ligand Trajectories in Molecular Dynamics

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00159816%3A_____%2F19%3A00072533" target="_blank" >RIV/00159816:_____/19:00072533 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/68407700:21230/19:00335521 RIV/00216224:14330/19:00107231

Výsledek na webu

<a href="http://dx.doi.org/10.1109/PacificVis.2019.00032" target="_blank" >http://dx.doi.org/10.1109/PacificVis.2019.00032</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1109/PacificVis.2019.00032" target="_blank" >10.1109/PacificVis.2019.00032</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Visual Analysis of Ligand Trajectories in Molecular Dynamics

Popis výsledku v původním jazyce

In many cases, protein reactions with other small molecules (ligands) occur in a deeply buried active site. When studying these types of reactions, it is crucial for biochemists to examine trajectories of ligand motion. These trajectories are predicted with in-silico methods that produce large ensembles of possible trajectories. In this paper, we propose a novel approach to the interactive visual exploration and analysis of large sets of ligand trajectories, enabling the domain experts to understand protein function based on the trajectory properties. The proposed solution is composed of multiple linked 2D and 3D views, enabling the interactive exploration and filtering of trajectories in an informed way. In the workflow, we focus on the practical aspects of the interactive visual analysis specific to ligand trajectories. We adapt the small multiples principle to resolve an overly large number of trajectories into smaller chunks that are easier to analyze. We describe how drill-down techniques can be used to create and store selections of the trajectories with desired properties, enabling the comparison of multiple datasets. In appropriately designed 2D and 3D views, biochemists can either observe individual trajectories or choose to aggregate the information into a functional boxplot or density visualization. Our solution is based on a tight collaboration with the domain experts, aiming to address their needs as much as possible. The usefulness of our novel approach is demonstrated by two case studies, conducted by the collaborating protein engineers.

Název v anglickém jazyce

Visual Analysis of Ligand Trajectories in Molecular Dynamics

Popis výsledku anglicky

In many cases, protein reactions with other small molecules (ligands) occur in a deeply buried active site. When studying these types of reactions, it is crucial for biochemists to examine trajectories of ligand motion. These trajectories are predicted with in-silico methods that produce large ensembles of possible trajectories. In this paper, we propose a novel approach to the interactive visual exploration and analysis of large sets of ligand trajectories, enabling the domain experts to understand protein function based on the trajectory properties. The proposed solution is composed of multiple linked 2D and 3D views, enabling the interactive exploration and filtering of trajectories in an informed way. In the workflow, we focus on the practical aspects of the interactive visual analysis specific to ligand trajectories. We adapt the small multiples principle to resolve an overly large number of trajectories into smaller chunks that are easier to analyze. We describe how drill-down techniques can be used to create and store selections of the trajectories with desired properties, enabling the comparison of multiple datasets. In appropriately designed 2D and 3D views, biochemists can either observe individual trajectories or choose to aggregate the information into a functional boxplot or density visualization. Our solution is based on a tight collaboration with the domain experts, aiming to address their needs as much as possible. The usefulness of our novel approach is demonstrated by two case studies, conducted by the collaborating protein engineers.

Druh

D - Stať ve sborníku

CEP obor

—

OECD FORD obor

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

Projekt

<a href="/cs/project/GA17-07690S" target="_blank" >GA17-07690S: Metody identifikace a vizualizace tunelů pro flexibilní ligandy v dynamických proteinech</a><br>

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2019

Kód důvěrnosti údajů

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

Název statě ve sborníku

2019 IEEE PACIFIC VISUALIZATION SYMPOSIUM (PACIFICVIS 2019)

ISBN

978-1-5386-9226-4

ISSN

2165-8765

e-ISSN

—

Počet stran výsledku

10

Strana od-do

212-221

Název nakladatele

IEEE

Místo vydání

NEW YORK

Místo konání akce

Chulalongkorn Univ

Datum konání akce

23. 4. 2019

Typ akce podle státní příslušnosti

WRD - Celosvětová akce

Kód UT WoS článku

000502097000020