MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data 2020

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https://diglib.eg.org/handle/10.2312/2632906

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Browsing MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data 2020 by Title

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    Improved Umbrella Visualization implemented in UnityMol gives valuable insight on sugar/protein interplay
    (The Eurographics Association, 2020) Besançon, Camille; Wong, Hua; Rao, Rajas; Dauchez, Manuel; Belloy, Nicolas; Prévoteau-Jonquet, Jessica; Baud, Stéphanie; Byška, Jan and Krone, Michael and Sommer, Björn
    Among the various post-translational modifications, N-glycosylations are particularly important. They are linked to asparagine residues and their function as well as the one of the protein can be altered by modifications such as sialic acid hydrolysis. Since in vitro studies of N-glycans can be a challenging process (glycosylation chains have a great diversity and contain many reactive groups), in silico characterization using molecular dynamics simulation seems to be a good tool capable of overcoming experimental shortcomings thanks to exhaustive conformational samplings. In this paper, the Umbrella Visualization, a recent implementation into the molecular viewer UnityMol, is presented. This new and original visualization method is offering the possibility to follow and decipher the dynamics of very flexible sugar chains and enable the identification of the protein surface covered and potentially impacted by glycans. The latest module, described here and integrated within the Umbrella Visualization, complements the original statistical approach and allows for a meaningful description of glycan/protein interplay by combining, with shadow mapping, labelling, and hydrophobic properties of the surrounding aminoacids.
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    Mesoscope: A Web-based Tool for Mesoscale Data Integration and Curation
    (The Eurographics Association, 2020) Autin, Ludovic; Maritan, Martina; Barbaro, Brett A.; Gardner, Adam; Olson, Arthur J.; Sanner, Michel; Goodsell, David S.; Byška, Jan and Krone, Michael and Sommer, Björn
    Interest is growing for 3D models of the biological mesoscale, the intermediate scale between the nanometer scale of molecular structure and micrometer scale of cellular biology. However, it is currently difficult to gather, curate and integrate all the data required to define such models. To address this challenge we developed Mesoscope (mesoscope.scripps.edu/beta), a web-based data integration and curation tool. Mesoscope allows users to begin with a listing of molecules (such as data from proteomics), and to use resources at UniProt and the PDB to identify, prepare and validate appropriate structures and representations for each molecule, ultimately producing a portable output file used by CellPACK and other modeling tools for generation of 3D models of the biological mesoscale. The availability of this tool has proven essential in several exploratory applications, given the high complexity of mesoscale models and the heterogeneity of the available data sources.
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    Molecular Binding in a Visuohaptic Environment: An Enhanced Approach in STEM Learning
    (The Eurographics Association, 2020) Yasmin, Shamima; Quick, Rhianna; Byška, Jan and Krone, Michael and Sommer, Björn
    Learning science, technology, engineering, and mathematics (STEM) can be dull in the absence of adequate incentives; students may lose interest in STEM subjects during their high school education. This could result in a decline in enrollment in STEM fields in postsecondary education and employment as well. However, learning can be reinforced in a multimodal environment. For example, a haptic virtual environment (VE) that incorporates both vision and touch can provide better affordance in learning. This multimodal VE may help students to better understand the underlying concepts of molecular formation while pursuing chemistry and related subjects at the secondary level. Visuohaptics may work as an incentive in learning complex molecular structures and become a source of edutainment and extra motivation for students. Thus, a multimodal VE enhances attentiveness and interest among students in pursuing STEM fields in secondary and postsecondary education.
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    MolVa 2020: Frontmatter
    (The Eurographics Association, 2020) Byška, Jan; Krone, Michael; Sommer, Björn; Byška, Jan and Krone, Michael and Sommer, Björn
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    The Vesicle Builder - A Membrane Packing Algorithm for the CELLmicrocosmos MembraneEditor
    (The Eurographics Association, 2020) Giuliari, Beatrice; Kösters, Manuel; Zhou, Jan; Dingersen, Tim; Heissmann, André; Rotzoll, Ralf; Krüger, Jens; Giorgetti, Alejandro; Sommer, Björn; Byška, Jan and Krone, Michael and Sommer, Björn
    For a long time, the major focus of membrane simulations was laid on rectangular membrane patches based on the fluid mosaic model. Because of the computational performance of today's computer hardware, it is now possible to generate and simulate larger structures, such as vesicles or micelles. Yet, there are no approaches available to generate these partly complex structures in a convenient and interactive way using WYSIWYG methods and exporting it to PDB format. The CELLmicrocosmos 2.2 MembraneEditor was originally developed for the interactive computation of heterogeneous rectangular membrane patches, solving 2.5D packing problems. Now, its packing capabilities were extended into the third dimension by introducing the Vesicle Builder which is optimized for the computation of vesicular mono- or bilayer membranes. The shape computation is based on an ellipsoid formula enabling the generation of vesicles featuring different lipid compositions, shapes and sizes. More complex shapes can be generated by combining different shapes. Moreover, extended shape customization is possible by modifying and extending the algorithm. Three application cases are discussed: 1) Different potential vesicular configurations including wavy, ellipsoid, enclosing and modular structures are modelled and shortly discussed; 2) To evaluate the compatibility of the Vesicle Builder with simulation tools, a three-component vesicle was modelled and successfully simulated. 3) To show the capability to generate large structures, a vesicle with a radius of 370 Å was generated, consisting of approx. 50,000 lipids and 2 million atoms, respectively. The MembraneEditor as well as the Vesicle Builder plugin can be downloaded from https://Cm2.CELLmicrocosmos.org