Visual exploration of large normal mode spaces to study protein flexibility

Result code in 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>

Result on the web

<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>

Result language

angličtina

Original language name

Visual exploration of large normal mode spaces to study protein flexibility

Original language description

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.

Czech name

—

Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10200 - Computer and information sciences

Project

—

Continuities

S - Specificky vyzkum na vysokych skolach

Publication year

2020

Confidentiality

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

Name of the periodical

Computers & Graphics

ISSN

0097-8493

e-ISSN

—

Volume of the periodical

90

Issue of the periodical within the volume

August

Country of publishing house

NL - THE KINGDOM OF THE NETHERLANDS

Number of pages

11

Pages from-to

73-83

UT code for WoS article

000558004700010

EID of the result in the Scopus database

2-s2.0-85085769658