Experiments with structural & mechanistic focus.
Biophysical models of specificity.
DNA targeting specificity of RNA-guided Cas9 nucleases (https://crispr.bme.gatech.edu/): Contains experimental data about the specificity. They also have a server based on the data.
A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation: This is a simple biophysical model used to predict the specificity of the sgRNA based on the sequence. They split the process in 3 steps and add the free energy change of each process to calculate a binding energy.
High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects : Mutations on residues that bind to the phosphate backbone of the DNA can improve the specificity.
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.)
Mechanistic Insight into Catalytic Activity of BBA-Metallonucleases (This model system, Vibrio vulnificus, is thought to have the same cleavage mechanism as the HNH domain.)
Catalytic Mechanisms of Restriction and Homing Endonucleases (A general overview of both one- and two-metal reactions, not specifically theory-oriented.)
The Nucleophile in Ribozyme Catalysis (Not directly related, but an analogous cleavage reaction. The SI also has lots of detailed information on their QM/MM simulations.)
RNA coarse grain models: