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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3110985/
QM:MM
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Simulations
Gamess+Tinker http://cfm.ehu.es/ricardo/master/intranet_ESCMAN/WinGAMESS/manuals/simomm.pdf (advantages: free, disadvantages: might not run well )
Gaussian+Gromacs http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMM (advantages: will work well, Scuseria will likely help; disadvantages: will likely be limited to Rice U comp. resources.)
RNA coarse grain models:
http://pubs.acs.org/doi/abs/10.1021/jp104926t
http://rnajournal.cshlp.org/content/14/6/1164.long
Layman news:
https://www.wired.com/2017/06/crispr-mutations/
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