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

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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.
A Massively Parallel CUDA Algorithm to Compute and Visualize the Solvent Excluded Surface for Dynamic Molecular Data
(The Eurographics Association, 2019) Schäfer, Marco; Krone, Michael; Byska, Jan and Krone, Michael and Sommer, Björn
The interactive visualization of molecular surfaces can help users to understand the dynamic behavior of proteins in molecular dynamics simulations. These simulations play an important role in biochemical and pharmaceutical research, e.g. in drug design. The efficient calculation of molecular surfaces in a fast and memory-saving way is a challenging task. For example, to gain a detailed understanding of complex diseases like Alzheimer, conformational changes and spatial interactions between molecules have to be investigated. Molecular surfaces, such as Solvent Excluded Surfaces (SES), are instrumental for identifying structures such as tunnels or cavities that critically influence transport processes and docking events, which might induce enzymatic reactions. Therefore, we developed a highly parallelized algorithm that exploits the massive computing power of modern graphics hardware. Our analytical algorithm is suitable for the real-time computation of dynamic SES based on many time steps, as it runs interactively on a single consumer GPU for more than 20 k atoms.
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.
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.
PBmapclust: Mapping and Clustering the Protein Conformational Space Using a Structural Alphabet
(The Eurographics Association, 2019) Vetrivel, Iyanar; Hoffmann, Lionel; Guegan, Sean; Offmann, Bernard; Laurent, Adele D.; Byska, Jan and Krone, Michael and Sommer, Björn
Analyzing the data from molecular dynamics simulation of biological macromolecules like proteins is challenging. We propose a simple tool called PBmapclust that is based on a well established structural alphabet called Protein blocks (PB). PBs help in tracing the trajectory of the protein backbone by categorizing it into 16 distinct structural states. PBmapclust provides a time vs. amino acid residue plot that is color coded to match each of the PBs. Color changes correspond to structural changes, giving a visual overview of the simulation. Further, PBmapclust enables the user to "map" the conformational space sampled by the protein during the MD simulation by clustering the conformations. The ability to generate sub-maps for specific residues and specific time intervals allows the user to focus on residues of interest like for active sites or disordered regions. We have included an illustrative case study to demonstrate the utility of the tool. It describes the effect of the disordered domain of a HSP90 co-chaperone on the conformation of its active site residues. The scripts required to perform PBmapclust are made freely available under the GNU general public license.
QuickSES: A Library for Fast Computation of Solvent Excluded Surfaces
(The Eurographics Association, 2019) Martinez, Xavier; Krone, Michael; Baaden, Marc; Byska, Jan and Krone, Michael and Sommer, Björn
Recently, several fast methods to compute Solvent Excluded Surfaces (SES) on GPUs have been presented. While these published methods reportedly yield interesting and useful results, up to now no public, freely accessible implementation of a fast and opensource SES mesh computation method that runs on GPUs is available. Most molecular viewers, therefore, still use legacy CPU methods that run only on a single core, without GPU acceleration. In this paper, we present an in-depth explanation and a fully open-source CUDA implementation of the fast, grid-based computation method proposed by Hermosilla et al. [HKG*17]. Our library called QuickSES runs on GPUs and is distributed with a permissive license. It comes with a standalone program that reads Protein Data Bank (PDB) files and outputs a complete SES mesh as a Wavefront OBJ file. Alternatively it can directly be integrated in classical molecular viewers as shared library. We demonstrate the low memory consumption to enable execution on lower-end GPUs, and compare the runtime speed-up to available state-of-the-art tools.
A Virtual and Mixed Reality Platform for Molecular Design & Drug Discovery - Nanome Version 1.24
(The Eurographics Association, 2023) Bennie, Simon J.; Maritan, Martina; Gast, Jonathon; Loschen, Marc; Gruffat, Daniel; Bartolotta, Roberta; Hessenauer, Sam; Leija, Edgardo; McCloskey, Steve; Byška, Jan; Krone, Michael; Sommer, Björn
The success of the design and improvement of nanoscale biomolecules like proteins and small molecule drugs relies on a proper understanding of their three-dimensional structures. Nanome's virtual reality/mixed reality (VR/MR) platform provides an immersive and collaborative environment that offers a unique view into the nanoscale world. The platform enables faster and more effective ideation, improved communication of scientific concepts, and multiple tools for lead optimization of molecules. The latest 1.24 version of the Nanome platform integrates multi-user collaboration, mixed reality, enhanced avatars, and a flexible Python API for easy integration with various modeling techniques. We describe key elements of this state-of-the-art framework and how it can accelerate the pace of discovery through empowering industry-standard algorithms across domains of digital science. Nanome is available for download at https://home.nanome.ai/setup.

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