Recent Submissions

  • PBmapclust: Mapping and Clustering the Protein Conformational Space Using a Structural Alphabet 

    Vetrivel, Iyanar; Hoffmann, Lionel; Guegan, Sean; Offmann, Bernard; Laurent, Adele D. (The Eurographics Association, 2019)
    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 ...
  • MolFind - Integrated Multi-Selection Schemes for Complex Molecular Structures 

    Skånberg, Robin; Linares, Mathieu; Falk, Martin; Hotz, Ingrid; Ynnerman, Anders (The Eurographics Association, 2019)
    Selecting components and observing changes of properties and configurations over time is an important step in the analysis of molecular dynamics (MD) data. In this paper, we present a selection tool combining text-based ...
  • QuickSES: A Library for Fast Computation of Solvent Excluded Surfaces 

    Martinez, Xavier; Krone, Michael; Baaden, Marc (The Eurographics Association, 2019)
    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 ...
  • A Massively Parallel CUDA Algorithm to Compute and Visualize the Solvent Excluded Surface for Dynamic Molecular Data 

    Schäfer, Marco; Krone, Michael (The Eurographics Association, 2019)
    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 ...
  • MolVa 2019: Frontmatter 

    Byska, Jan; Krone, Michael; Sommer, Björn (The Eurographics Association, 2019)
  • Mol*: Towards a Common Library and Tools for Web Molecular Graphics 

    Sehnal, David; Rose, Alexander; Koca, Jaroslav; Burley, Stephen; Velankar, Sameer (The Eurographics Association, 2018)
    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 ...
  • VIA-MD: Visual Interactive Analysis of Molecular Dynamics 

    Skånberg, Robin; Linares, Mathieu; König, Carolin; Norman, Patrick; Jönsson, Daniel; Hotz, Ingrid; Ynnerman, Anders (The Eurographics Association, 2018)
    We present a visual exploration environment tailored for large-scale spatio-temporal molecular dynamics simulation data. The environment is referred to as VIA-MD (visual interactive analysis of molecular dynamics) and has ...
  • Atomic Accessibility Radii for Molecular Dynamics Analysis 

    Lindow, Norbert; Baum, Daniel; Hege, Hans-Christian (The Eurographics Association, 2018)
    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, ...
  • An Accelerated Online PCA with O(1) Complexity for Learning Molecular Dynamics Data 

    Alakkari, Salaheddin; Dingliana, John (The Eurographics Association, 2018)
    In this paper, we discuss the problem of decomposing complex and large Molecular Dynamics trajectory data into simple low-resolution representation using Principal Component Analysis (PCA). Since applying standard PCA for ...
  • MolVA 2018: Frontmatter 

    Byška, Jan; Krone, Michael; Sommer, Björn (The Eurographics Association, 2018)