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

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Browsing MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data by Subject "Bioinformatics"

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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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    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.
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    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.