A Knowledge-Based Method for Instantiating Full Atomic Detail into Coarse Grain RNA Structure Models
This work uses a knowledge-based approach to instantiate full atomic detail into coarse grain templates of RNA 3D structures. Any atom-based coarse-graining scheme can be used as input for our method. The result is a full atomic structure.
The software is now available independently of NAST. Please follow the download link to access the C2A package. Supporting material is under the Documents link.
We currently support Unix and Mac OS X platforms.
The C2A package will take you as far as adding atomic detail, but you will need to use a physics-based MD engine to minimize the structures. The easiest way to do this is to install the Zephyr package from simtk, which is a free, user-friendly, graphical interface to GROMACS. The harder way (and the way used in the C2A paper) is to use gromacs directly. We have posted directions for how to do this under the documents section.
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