3D RNA Modeling and Simulation Workshop
June 19, 2009

The structure and dynamics of molecules is central to understanding biological function, and yet most experimentalists find existing structural modeling tools excessively limited in scope and difficult to use. In Simbios’ 3D RNA Modeling and Simulation Workshop, participants learned new tools that enable them to generate structures and dynamical trajectories based on thier hypotheses, limited experimental information, and/or initial coordinates. The presented molecular modeling tools were designed to be easily applied by experimentalists to problems of current biological interest.


  • An “Introduction to 3D RNA Modeling and Simulation” lecture, given by Dr. Russ Altman, Chairman of the Department of Bioengineering and Director of the Biomedical Informatics Training Program at Stanford University.

  • Learn to use three different tools to meet different modeling and simulation needs
      • Nucleic Acid Simulation Tool (NAST): Generates a large number of conformationally diverse coarse-grained 3D structures that satisfy user-provided secondary and tertiary contacts. [1]
      • RNABuilder: constructs structural models of RNA by enforcing user-provided base pairing interactions and other structural constraints. Key to the algorithm's effectiveness is its ability to enforce a folding pathway that is automatically computed or provided by the user.
      • OpenMM Zephyr: Generates a full atomic simulation using a version of the GROMACS molecular dynamics package that runs on GPUs, producing speed-ups of over 700X in some cases.
  • Participants worked with the tool developers to generate 3D models and simulations using their own data

  • See the detailed agenda

    Materials from the workshop

    Click here to access the slides, videos and other materials from the workshop.

    [1] Jonikas, MA, et al., “Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters,” RNA, 2009, 15:189-199