Reviews
CRISPR–Cas9 Structures and Mechanisms
Simulations
Cas9-catalyzed DNA Cleavage Generates Staggered Ends: Evidence from Molecular Dynamics Simulations
CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations
Experiments with structural & mechanistic focus.
DNA interrogation by the CRISPR RNA-guided endonuclease Cas9
Massively Parallel Biophysical Analysis of CRISPR-Cas Complexes on Next Generation Sequencing Chips
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.
Cleavage
https://www.nature.com/articles/srep37584.pdf
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3110985/
QM:MM 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/