Visual exploration of large normal mode spaces to study protein flexibility

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14330%2F20%3A00116311" target="_blank" >RIV/00216224:14330/20:00116311 - isvavai.cz</a>

Výsledek na webu

<a href="http://dx.doi.org/10.1016/j.cag.2020.05.025" target="_blank" >http://dx.doi.org/10.1016/j.cag.2020.05.025</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.cag.2020.05.025" target="_blank" >10.1016/j.cag.2020.05.025</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Visual exploration of large normal mode spaces to study protein flexibility

Popis výsledku v původním jazyce

When studying the function of proteins, biochemists utilize normal mode decomposition to enable the analysis of structural changes on time scales that are too long for molecular dynamics simulation. Such a decomposition yields a high-dimensional parameter space that is too large to be analyzed exhaustively. We present a novel approach to reducing and exploring this vast space through the means of interactive visualization. Our approach enables the inference of relevant protein function from single structure dynamics through protein tunnel analysis while considering normal mode combinations spanning the whole normal modes space. Our solution, based on multiple linked 2D and 3D views, enables the quick and flexible exploration of individual modes and their effect on the dynamics of tunnels with relevance for the protein function. Once an interesting motion is identified, the exploration of possible normal mode combinations is steered via a visualization-based recommendation system. This helps to quickly identify a narrow, yet relevant set of normal modes that can be investigated in detail. Our solution is the result of close cooperation between visualization and the domain. The versatility and efficiency of our approach are demonstrated in several case studies.

Název v anglickém jazyce

Visual exploration of large normal mode spaces to study protein flexibility

Popis výsledku anglicky

When studying the function of proteins, biochemists utilize normal mode decomposition to enable the analysis of structural changes on time scales that are too long for molecular dynamics simulation. Such a decomposition yields a high-dimensional parameter space that is too large to be analyzed exhaustively. We present a novel approach to reducing and exploring this vast space through the means of interactive visualization. Our approach enables the inference of relevant protein function from single structure dynamics through protein tunnel analysis while considering normal mode combinations spanning the whole normal modes space. Our solution, based on multiple linked 2D and 3D views, enables the quick and flexible exploration of individual modes and their effect on the dynamics of tunnels with relevance for the protein function. Once an interesting motion is identified, the exploration of possible normal mode combinations is steered via a visualization-based recommendation system. This helps to quickly identify a narrow, yet relevant set of normal modes that can be investigated in detail. Our solution is the result of close cooperation between visualization and the domain. The versatility and efficiency of our approach are demonstrated in several case studies.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10200 - Computer and information sciences

Projekt

—

Návaznosti

S - Specificky vyzkum na vysokych skolach

Rok uplatnění

2020

Kód důvěrnosti údajů

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

Název periodika

Computers & Graphics

ISSN

0097-8493

e-ISSN

—

Svazek periodika

90

Číslo periodika v rámci svazku

August

Stát vydavatele periodika

NL - Nizozemsko

Počet stran výsledku

11

Strana od-do

73-83

Kód UT WoS článku

000558004700010

EID výsledku v databázi Scopus

2-s2.0-85085769658