Team:Waterloo/Modeling/PAM Flexibility
Modelling Engineered Cas9 PAM Flexibility
Copy and past code from this page as a template for the rest of the site
Why is it important to do this? / Is it possible
PAM Sites Differ between Natural Cas9 PRoteins
Engineered SpyCas9 NGAG and NGA
Computational Engineering of PAM Flexibility
Modelling Binding with PyMOL and PyRosetta
Canonical molecular dynamics data, mention source of PDB
Mutating PAM sites within PDB
Available PAM Affinity Data
Mention Klienstiver and
Engineering Pipeline
Summarize whole approach
Model Validation
Choice of DNA Mutation Software
Chimera VS 3DNA, give stats details
Patterns of Variation between Simulations
Simulations are Monte Carlo, we analyzed the differences between them
Wild-Type Cas9 PAM Affinities are Reproduced
Report Kendall's Tau, Pearson, Clustering Results
Mutant Cas9 PAM Affinities show Mixed Results
Mutating VQR/EQR, how EQR and VQR mutants change Cas9 visualizations, measures of distance from DNA bases to binding sites in the Cas9
Framework and Future Work
Proposed Tool
Link to software page re:pyrosetta
Future Work
Talk about adding other info like Gibb's Free Energy
Show a few graphs from Kleinstiver and link to dataset encouraging others to use