SimVIZ – A Desktop Virtual Environment for Visualization and Analysis of Protein Multiple Simulation Trajectories

  • Ricardo M. Czekster
  • Osmar Norberto de Souza
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3980)


In silico protein conformation simulation generates massive amounts of data which needs to be properly visualized and analyzed. We are applying Desktop Information-Rich Virtual Environments (Desktop IRVE’s) techniques and concepts to aid multiple trajectory simulation analysis, improving user experience and developing a problem-solving environment to help the decision making process. We will present SimVIZ, a tool which integrates visualization to simulation analysis, improving previous knowledge about trajectories. This environment shows informative panels, Contact Maps, RMSD charts, the Ramachandran Plot and a Parallel Coordinate multidimensional visualization of simulation output in a single rendering scene. SimVIZ also opens multiple trajectories along with user associated information concerning many aspects of the simulation. SimVIZ is an integrated problem solving environment of multiple trajectories of protein simulations, offering various kinds of analysis and visualization tools used by the community to validate protein structures or to gather a better understanding of the protein folding process.


Virtual Environment Ramachandran Plot Simulation Trajectory Information Visualization Visual Molecular Dynamics 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Ricardo M. Czekster
    • 1
  • Osmar Norberto de Souza
    • 1
  1. 1.Laboratório de BioinformáticaModelagem e Simulação de Biossistemas – LABIO, PPGCC – FACIN, PUCRSPorto AlegreBrasil

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