Now showing items 1-12 of 12

    • A general illumination model for molecular visualization 

      Hermosilla Casajús, Pedro; Vázquez Alcocer, Pere Pau; Vinacua Pla, Álvaro; Ropinski, Timo (2018-06)
      Article
      Open Access
      Several visual representations have been developed over the years to visualize molecular structures, and to enable a better understanding of their underlying chemical processes. Today, the most frequently used atom-based ...
    • An experimental study on the effects of shading in 3D perception of volumetric models 

      Díaz Iriberri, José; Ropinski, Timo; Navazo Álvaro, Isabel; Gobbetti, Enrico; Vázquez Alcocer, Pere Pau (Springer, 2017-01)
      Article
      Restricted access - publisher's policy
      Throughout the years, many shading techniques have been developed to improve the conveying of information in volume visualization. Some of these methods, usually referred to as realistic, are supposed to provide better ...
    • Improving perception of molecular surface visualizations by incorporating translucency effects 

      Hermosilla Casajús, Pedro; Maisch, Sebastian; Vázquez Alcocer, Pere Pau; Ropinski, Timo (European Association for Computer Graphics (Eurographics), 2018)
      Conference report
      Open Access
      Molecular surfaces are a commonly used representation in the analysis of molecular structures as they provide a compact description of the space occupied by a molecule and its accessibility. However, due to the high ...
    • Interactive GPU-based generation of solvent-excluded surfaces 

      Hermosilla Casajús, Pedro; Krone, Michael; Guallar, Víctor; Vázquez Alcocer, Pere Pau; Vinacua Pla, Álvaro; Ropinski, Timo (Springer, 2017-05-08)
      Article
      Open Access
      The solvent-excluded surface (SES) is a popular molecular representation that gives the boundary of the molecular volume with respect to a specific solvent. SESs depict which areas of a molecule are accessible by a specific ...
    • Interactive GPU-based generation of solvent-excluded surfaces 

      Hermosilla, Pedro; Krone, Michael; Guallar, Victor; Vázquez, Pere-Pau; Vinacua Pla, Álvaro; Ropinski, Timo (Springer International Publishing, 2017-06)
      Article
      Open Access
      The solvent-excluded surface (SES) is a popular molecular representation that gives the boundary of the molecular volume with respect to a specific solvent. SESs depict which areas of a molecule are accessible by a specific ...
    • Intrinsic-extrinsic convolution and pooling for learning on 3D protein structures 

      Hermosilla Casajús, Pedro; Schäfer, Marco; Lang, Matej; Fackelmann, Gloria; Vázquez Alcocer, Pere Pau; Kozliková, Barbora; Krone, Michael; Ritschel, Tobias; Ropinski, Timo (OpenReview.net, 2021)
      Conference lecture
      Open Access
      Proteins perform a large variety of functions in living organisms and thus play a key role in biology. However, commonly used algorithms in protein learning were not specifically designed for protein data, and are therefore ...
    • Monte Carlo convolution for learning on non-uniformly sampled point clouds 

      Hermosilla Casajús, Pedro; Ristchel, Tobias; Vázquez Alcocer, Pere Pau; Vinacua Pla, Álvaro; Ropinski, Timo (2018-11)
      Article
      Open Access
      Deep learning systems extensively use convolution operations to process input data. Though convolution is clearly defined for structured data such as 2D images or 3D volumes, this is not true for other data types such as ...
    • Perceptual effects of volumetric shading models in stereoscopic desktop-based environments 

      Díaz Iriberri, José; Ropinski, Timo; Navazo Álvaro, Isabel; Gobbetti, Enrico; Vázquez Alcocer, Pere Pau (2015)
      Conference lecture
      Open Access
      Throughout the years, many shading techniques have been developed to improve the conveying of information in Volume Visualization. Some of these methods, usually referred to as realistic, are supposed to provide better ...
    • Physics-Based Visual Characterization of Molecular Interaction Forces 

      Hermosilla, Pedro; Estrada, Jorge; Guallar, Victor; Ropinski, Timo; Vinacua, Álvar; Vázquez, Pere-Pau (IEEE, 2017-01)
      Article
      Open Access
      Molecular design procedures, such as drug design and protein engineering’ are complex processes, largely benefiting from computational resources but also from human analysis. In drug design, for example, a costly iterative ...
    • Physics-based visual characterization of molecular interaction forces 

      Hermosilla, Pedro; Estrada, Jorge; Guallar, Víctor; Ropinski, Timo; Vinacua Pla, Álvaro; Vázquez Alcocer, Pere Pau (2017-01-01)
      Article
      Open Access
      Molecular simulations are used in many areas of biotechnology, such as drug design and enzyme engineering. Despite the development of automatic computational protocols, analysis of molecular interactions is still a major ...
    • Real-time molecular visualization supporting diffuse interreflections and ambient occlusion 

      Skanberg, Robin; Vázquez Alcocer, Pere Pau; Guallar, Victor; Ropinski, Timo (2016-01-01)
      Article
      Open Access
      Today molecular simulations produce complex data sets capturing the interactions of molecules in detail. Due to the complexity of this time-varying data, advanced visualization techniques are required to support its visual ...
    • Visualization of large molecular trajectories 

      Duran Rosich, David; Hermosilla Casajús, Pedro; Ropinski, Timo; Kozliková, Barbora; Vinacua Pla, Álvaro; Vázquez Alcocer, Pere Pau (2018-09-06)
      Article
      Open Access
      The analysis of protein-ligand interactions is a time-intensive task. Researchers have to analyze multiple physico-chemical properties of the protein at once and combine them to derive conclusions about the protein-ligand ...