MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data 2018

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https://diglib.eg.org/handle/10.2312/2632405

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Browsing MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data 2018 by Subject "Computing methodologies"

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    Atomic Accessibility Radii for Molecular Dynamics Analysis
    (The Eurographics Association, 2018) Lindow, Norbert; Baum, Daniel; Hege, Hans-Christian; Jan Byska and Michael Krone and Björn Sommer
    In molecular structure analysis and visualization, the molecule's atoms are often modeled as hard spheres parametrized by their positions and radii. While the atom positions result from experiments or molecular simulations, for the radii typically values are taken from literature. Most often, van der Waals (vdW) radii are used, for which diverse values exist. As a consequence, different visualization and analysis tools use different atomic radii, and the analyses are less objective than often believed. Furthermore, for the geometric accessibility analysis of molecular structures, vdW radii are not well suited. The reason is that during the molecular dynamics simulation, depending on the force field and the kinetic energy in the system, non-bonded atoms can come so close to each other that their vdW spheres intersect. In this paper, we introduce a new kind of atomic radius, called 'atomic accessibility radius', that better characterizes the accessibility of an atom in a given molecular trajectory. The new radii reflect the movement possibilities of atoms in the simulated physical system. They are computed by solving a linear program that maximizes the radii of the atoms under the constraint that non-bonded spheres do not intersect in the considered molecular trajectory. Using this data-driven approach, the actual accessibility of atoms can be visualized more precisely.
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    Mol*: Towards a Common Library and Tools for Web Molecular Graphics
    (The Eurographics Association, 2018) Sehnal, David; Rose, Alexander; Koca, Jaroslav; Burley, Stephen; Velankar, Sameer; Jan Byska and Michael Krone and Björn Sommer
    Advances in experimental techniques are providing access to structures of ever more complex and larger macromolecular systems. Web-browser based visualization and analysis of macromolecular structures and associated data represents a crucial step in gaining knowledge from these data. A common library and a set of tools for working with such macromolecular data sets would streamline this step. We present a project called Mol* (/'mol-star/) whose goal is to provide a common library and a set of tools for macromolecular data visualization and analysis. The project includes modules for data storage, in-memory representation, query language, UI state management, and visualization; and tools for efficient data access.