Provide tutorials and other workshop materials for 3D RNA Modeling and Simulation Tools: NAST/C2A, RNABuilder, and OpenMM Zephyr
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, you will learn new tools that enable you to generate structures and dynamical trajectories based on your hypotheses, limited experimental information, and/or initial coordinates. The presented molecular modeling tools are designed to be easily applied by experimentalists to problems of current biological interest.
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There are three different tools to meet your 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.
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.
This project provides the slides and other training materials created for these three tools for use in the June 2009 workshop.