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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, participants will learn new tools that enable them to generate structures and dynamical trajectories based on their 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.

If you attended the workshop please fill out the survey by going to https://simtk.org/docman/?group_id=489.

Downloads

There are three different tools to meet your different modeling and simulation needs:

Nucleic Acid Simulation Tool (NAST): (https://simtk.org/home/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: (https://simtk.org/home/rnatoolbox), 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: ((https://simtk.org/home/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.

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Related Projects

The project owner recommends the following other projects:

OpenMM Zephyr

MMB (MacroMoleculeBuilder)

NAST (The Nucleic Acid Simulation Tool)

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