Generating 3-D models of RNA from limited experimental data
The structure of RNA molecules is important to their function, but generating 3-D structural models of RNA remains a challenge. One approach to predicting these structures from the limited experimental data that is available is to apply an RNA-specific knowledge-based force field.
The nucleic acid simulation tool (NAST) has been written for this purpose and can be downloaded for free from https://simtk.org/home/nast. Read more about the validation of this tool in the article "Course-grained modeling of large RNA molecules with knowledge-based potentials and structural filters" in the Feb. 2009 issue of RNA (http://www.ncbi.nlm.nih.gov/pmc/artic....
Learn more about Simbios research on physics-based simulations of biological structures at http://simbios.stanford.edu.