Difference between revisions of "Team:Waterloo/Modeling/PAM Flexibility"

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<div class="container main-container">
 
<div class="container main-container">
  
−
     <h1>Modelling Engineered PAM Flexibility</h1>
+
     <h1>Modelling Engineered Cas9 PAM Flexibility</h1>
 
     <p>
 
     <p>
 
         Copy and past code from this page as a template for the rest of the site
 
         Copy and past code from this page as a template for the rest of the site
 
     </p>
 
     </p>
  
−
     <section id="headers" title="Headers">
+
     <section id="headers" title="Motivation">
−
        <h2>Headers</h2>
+
    <p>Why is it important to do this? / Is it possible</p>
 +
 
 +
    <p>PAM Sites Differ between Natural Cas9 PRoteins</p>
 +
    <p>Engineered SpyCas9 NGAG and NGA</p>
 +
    </section>
 +
 
 +
    <section id="headers" title="Computational Approach">
 +
    <h2>Computational Engineering of PAM Flexibility</h2>
 +
 
 +
    <h3>Modelling Binding with PyMOL and PyRosetta</h3>
 +
    <p>Canonical molecular dynamics data, mention source of PDB</p>
 +
    <p>Mutating PAM sites within PDB</p>
 +
   
 +
    <h3>Available PAM Affinity Data</h3>
 +
    <p>Mention Klienstiver and </p>
 +
 
 +
    <h3>Engineering Pipeline</h3>
 +
    <p>Summarize whole approach</p>
 +
    </section>
 +
 
 +
    <section id="headers" title="Model Validation">
 +
    <h2>Model Validation</h2>
 +
 
 +
    <h3>Choice of DNA Mutation Software</h3>
 +
    <p>Chimera VS 3DNA, give stats details</p>
 +
 
 +
    <h3>Patterns of Variation between Simulations</h3>
 +
    <p>Simulations are Monte Carlo, we analyzed the differences between them</p>
 +
 
 +
    <h3>Wild-Type Cas9 PAM Affinities are Reproduced</h3>
 +
    <p>Report Kendall's Tau, Pearson, Clustering Results</p>
 +
 
 +
    <h3>Mutant Cas9 PAM Affinities show Mixed Results</h3>
 +
    <p>Mutating VQR/EQR, how EQR and VQR mutants change Cas9 visualizations, measures of distance from DNA bases to binding sites in the Cas9</p>
 +
    </section>
 +
 
 +
    <section id="headers" title="Future Work">
 +
    <h2>Framework and Future Work</h2>
 +
 
 +
    <h3>Proposed Tool</h3>
 +
    <p>Link to software page re:pyrosetta</p>
 +
 
 +
    <h3>Future Work</h3>
 +
    <p>Talk about adding other info like Gibb's Free Energy</p>
 +
    <p>Show a few graphs from Kleinstiver and link to dataset encouraging others to use</p>
 
     </section>
 
     </section>
  

Revision as of 02:08, 16 September 2015

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

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