Visual exploration of large normal mode spaces to study protein
flexibility

J 2020

Visual exploration of large normal mode spaces to study protein flexibility

BEDOUCHA, Pierre, Reuter NATHALIE, Helwig HAUSER and Jan BYŠKA

Basic information

Original name

Visual exploration of large normal mode spaces to study protein flexibility

Authors

BEDOUCHA, Pierre (250 France), Reuter NATHALIE (250 France), Helwig HAUSER (40 Austria) and Jan BYŠKA (203 Czech Republic, belonging to the institution)

Edition

Computers & Graphics, Netherlands, Elsevier Science Direct, 2020, 0097-8493

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10200 1.2 Computer and information sciences

Country of publisher

Netherlands

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 1.936

RIV identification code

RIV/00216224:14330/20:00116311

Organization unit

Faculty of Informatics

DOI

http://dx.doi.org/10.1016/j.cag.2020.05.025

UT WoS

000558004700010

Keywords in English

Normal mode analysisProtein flexibilityMolecular visualizationCoordinated and multiple views

Změněno: 4/9/2020 17:29, RNDr. Jan Byška, Ph.D.

Abstract

V originále

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.

Citovat

BEDOUCHA, Pierre, Reuter NATHALIE, Helwig HAUSER and Jan BYŠKA. Visual exploration of large normal mode spaces to study protein flexibility. Computers & Graphics. Netherlands: Elsevier Science Direct, 2020, vol. 90, August, p. 73-83. ISSN 0097-8493. Available from: https://dx.doi.org/10.1016/j.cag.2020.05.025.

@article{1676647,
   author = {Bedoucha, Pierre and Nathalie, Reuter and Hauser, Helwig and Byška, Jan},
   article_location = {Netherlands},
   article_number = {August},
   doi = {http://dx.doi.org/10.1016/j.cag.2020.05.025},
   keywords = {Normal mode analysisProtein flexibilityMolecular visualizationCoordinated and multiple views},
   language = {eng},
   issn = {0097-8493},
   journal = {Computers & Graphics},
   title = {Visual exploration of large normal mode spaces to study protein flexibility},
   url = {http://dx.doi.org/10.1016/j.cag.2020.05.025},
   volume = {90},
   year = {2020}
}

TY  - JOUR
ID  - 1676647
AU  - Bedoucha, Pierre - Nathalie, Reuter - Hauser, Helwig - Byška, Jan
PY  - 2020
TI  - Visual exploration of large normal mode spaces to study protein flexibility
JF  - Computers & Graphics
VL  - 90
IS  - August
SP  - 73-83
EP  - 73-83
PB  - Elsevier Science Direct
SN  - 00978493
KW  - Normal mode analysisProtein flexibilityMolecular visualizationCoordinated and multiple views
UR  - http://dx.doi.org/10.1016/j.cag.2020.05.025
L2  - http://dx.doi.org/10.1016/j.cag.2020.05.025
N2  - 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.
ER  -

BEDOUCHA, Pierre, Reuter NATHALIE, Helwig HAUSER and Jan BYŠKA. Visual exploration of large normal mode spaces to study protein flexibility. \textit{Computers \&{} Graphics}. Netherlands: Elsevier Science Direct, 2020, vol.~90, August, p.~73-83. ISSN~0097-8493. Available from: https://dx.doi.org/10.1016/j.cag.2020.05.025.

Detailed Information on Publication Record