Visual exploration of large normal mode spaces to study protein flexibility

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.

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

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: 10200 1.2 Computer and information sciences
• Country of publisher: Netherlands
• Confidentiality degree: is not subject to a state or trade secret
• WWW: 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

Abstract

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.