3D RNA Modeling and Simulation Workshop
March 29, 2010

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 will learn 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] Related C2A tool can then add in full-atomic details.[2]
      • 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.[3]
      • OpenMM Zephyr: Generates a full atomic simulation using a version of the GROMACS molecular dynamics package that can be accelerated on GPUs.[4] Useful for augmenting RNA modeling tools like NAST and RNABuilder.
  • Hear about other RNA modeling tools

  • Participants work with the tool developers to generate 3D models and simulations using their own data

  • See the agenda.

    Workshop Logistics

    Where: The University of Illinois at Chicago

    When: March 29, 2010, 9am to 5pm


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    Additional Information: Attendees will be required to download the software onto their own laptops prior to 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

    [2] Jonikas, MA, et al., Knowledge-Based Instantiation of Full Atomic Detail into Coarse Grain RNA 3D Structural Models, Bioinformatics, 2009, 25(24):3259-3266.

    [3] Flores, S.C., Wan, Y., Russell, R., and Altman, R.B. (2010). Predicting RNA structure by multiple template homology modeling, Proceedings of the Pacific Symposium on Biocomputing, 15, 216-227.

    [4] Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, Legrand S, Beberg AL, Ensign DL, Bruns CM, Pande VS. (2009). Accelerating molecular dynamic simulation on graphics processing units, J Comput Chem, 30, 864-72