Visual Analysis of Ligand Trajectories in Molecular Dynamics

Result code in 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>

Alternative codes found

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

Result on the web

<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>

Result language

angličtina

Original language name

Visual Analysis of Ligand Trajectories in Molecular Dynamics

Original language description

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.

Czech name

—

Czech description

—

Type

D - Article in proceedings

CEP classification

—

OECD FORD branch

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

Project

<a href="/en/project/GA17-07690S" target="_blank" >GA17-07690S: Methods of Identification and Visualization of Tunnels for Flexible Ligands in Dynamic Proteins</a><br>

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2019

Confidentiality

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

Article name in the collection

2019 IEEE PACIFIC VISUALIZATION SYMPOSIUM (PACIFICVIS 2019)

ISBN

978-1-5386-9226-4

ISSN

2165-8765

e-ISSN

—

Number of pages

10

Pages from-to

212-221

Publisher name

IEEE

Place of publication

NEW YORK

Event location

Chulalongkorn Univ

Event date

Apr 23, 2019

Type of event by nationality

WRD - Celosvětová akce

UT code for WoS article

000502097000020