Visualization of Large Molecular Trajectories

DURAN, David, Pedro HERMOSILLA, Timo ROPINSKI, Barbora KOZLÍKOVÁ, Álvar VINACUA and Pere-Pau VAZQUEZ. Visualization of Large Molecular Trajectories. IEEE Transactions on Visualization and Computer Graphics. 2019, vol. 25, No 1, p. 987-996. ISSN 1077-2626. Available from: https://dx.doi.org/10.1109/TVCG.2018.2864851.

Basic information

• Original name: Visualization of Large Molecular Trajectories
• Authors: DURAN, David (724 Spain), Pedro HERMOSILLA (724 Spain), Timo ROPINSKI (276 Germany), Barbora KOZLÍKOVÁ (203 Czech Republic, belonging to the institution), Álvar VINACUA (724 Spain) and Pere-Pau VAZQUEZ (724 Spain, guarantor).
• Edition: IEEE Transactions on Visualization and Computer Graphics, 2019, 1077-2626.

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: United States of America
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Impact factor: Impact factor: 4.558
• RIV identification code: RIV/00216224:14330/19:00107176
• Organization unit: Faculty of Informatics
• Doi: http://dx.doi.org/10.1109/TVCG.2018.2864851
• UT WoS: 000452640000094
• Keywords in English: Trajectory;Proteins;Three-dimensional displays;Computational modeling;Visualization;Data models;Inspection
• Tags: International impact, Reviewed

Abstract

The analysis of protein-ligand interactions is a time-intensive task. Researchers have to analyze multiple physico-chemical properties of the protein at once and combine them to derive conclusions about the protein-ligand interplay. Typically, several charts are inspected, and 3D animations can be played side-by-side to obtain a deeper understanding of the data. With the advances in simulation techniques, larger and larger datasets are available, with up to hundreds of thousands of steps. Unfortunately, such large trajectories are very difficult to investigate with traditional approaches. Therefore, the need for special tools that facilitate inspection of these large trajectories becomes substantial. In this paper, we present a novel system for visual exploration of very large trajectories in an interactive and user-friendly way. Several visualization motifs are automatically derived from the data to give the user the information about interactions between protein and ligand. Our system offers specialized widgets to ease and accelerate data inspection and navigation to interesting parts of the simulation. The system is suitable also for simulations where multiple ligands are involved. We have tested the usefulness of our tool on a set of datasets obtained from protein engineers, and we describe the expert feedback.

Links

• GC18-18647J, research and development project: Name: Vizuální analýza interakcí proteinů a ligandů (Acronym: PROLINT)

Investor: Czech Science Foundation