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<h1>SETD8 wild-type apo and cofactor-bound, and mutant apo Folding@home simulations</h1> <h2>Main project repository</h2> <p>Additional project documentation, data, and scripts can be found here:</p> <p><a href="https://github.com/choderalab/SETD8-materials" rel="nofollow">https://github.com/choderalab/SETD8-materials</a></p> <h2>Trajectories without solvent</h2> <p>The following Folding@home projects were analyzed for the manuscript, and are made available here without solvent:</p> <h3>APO</h3> <p>wild type apo-SETD8</p> <p>11707:</p> <ul> <li>RUN0: 1ZKK A</li> <li>RUN2: 1ZKK B</li> <li>RUN3: 1ZKK D</li> <li>RUN4: 2BQZ A</li> <li>RUN5: 2BQZ E</li> <li>RUN6: 3F9W A</li> <li>RUN9: 3F9W D</li> <li>RUN11: 3F9X C</li> <li>RUN12: 3F9X B</li> <li>RUN13: 3F9X D</li> <li>RUN14: 3F9Y A</li> <li>RUN15: 3F9Y B</li> <li>RUN17: 3F9Z C</li> <li>RUN18: 3F9Z B</li> <li>RUN19: 3F9Z D</li> <li>RUN20: 4IJ8 A</li> <li>RUN21: 4IJ8 B</li> <li>RUN23: 6BOZ A</li> <li>RUN29: 6BOZ A</li> <li>RUN36-38: 6BOZ A</li> <li>RUN42-50: 4IJ8 A</li> <li>RUN51-59: 4IJ8 B</li> <li>RUN70-74: 6BOZ A</li> <li>RUN80-99: 5V2N A</li> <li>RUN100-109: 6BOZ B</li> <li>RUN110: 3F9W B</li> <li>RUN111: 3F9W C</li> <li>RUN112: 3F9X A</li> <li>RUN113-122: 5W1Y A</li> <li>RUN123-132: 5W1Y B</li> <li>RUN133: 1ZKK A</li> <li>RUN134: 3F9Z B</li> <li>RUN135-151: 4IJ8 A - 5W1Y A structural chimera</li> <li>RUN152-168: 5V2N A - 5W1Y A structural chimera</li> </ul> <p>11709:</p> <ul> <li>RUN0: 1ZKK A - 5V2N A structural chimera</li> <li>RUN1: 4IJ8 A - 5V2N A structural chimera</li> <li>RUN2: 6BOZ A - 5V2N A structural chimera</li> <li>RUN3: 4IJ8 A - 5V2N A structural chimera</li> </ul> <h3>SAM</h3> <p>cofactor (SAM)-bound SETD8</p> <p>11710:</p> <ul> <li>RUN0: 2BQZ A</li> <li>RUN2: 4IJ8 A</li> </ul> <h3>MUTANTS</h3> <p>mutant apo-SETD8 modeled on 1ZKK A</p> <p>11713:</p> <ul> <li>RUN0: A237V</li> <li>RUN1: R244S</li> <li>RUN2: I247L</li> <li>RUN3: E257K</li> <li>RUN4: T274I</li> <li>RUN5: R279Q</li> <li>RUN6: R279W</li> <li>RUN7: G280S</li> <li>RUN8: V283M</li> <li>RUN9: A296T</li> <li>RUN10: A301V</li> <li>RUN11: T309M</li> <li>RUN12: C324del</li> <li>RUN13: E330Q</li> <li>RUN14: R333C</li> <li>RUN15: R333L</li> <li>RUN16: L334P</li> <li>RUN17: H340D</li> <li>RUN18: D325Y</li> <li>RUN19: V356I</li> <li>RUN20: L359F</li> <li>RUN21: A368V</li> <li>RUN22: E372D</li> <li>RUN23: H388Q</li> </ul> <p>Each trajectory is available in the appropriate project folder:</p> <pre class="highlight"><code>SETD8 &lt;protein system&gt; &gt; &lt;project number&gt;</code></pre> <p>with trajectory files formatted as <code>run&lt;RUN&gt;-clone&lt;CLONE&gt;.h5</code>, with <code>&lt;RUN&gt;</code> indexing a set of trajectories started from the same conformation and <code>&lt;CLONE&gt;</code> denoting different replicates initiated from the same structure but different initial velocities.</p> <p>These trajectories are stored in <a href="http://mdtraj.org/latest/hdf5_format.html" rel="nofollow">MDTraj HDF5 format</a>. This is a compact, platform-portable format that contains both topology information (atom names, connectivity, and residue information) and trajectory data. You can use the freely-available <a href="http://mdtraj.org" rel="nofollow">MDTraj</a> package to convert to other popular trajectory formats.</p>
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