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<h1>AurA wild-type and mutant 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/AurA-materials" rel="nofollow">https://github.com/choderalab/AurA-materials</a></p> <h2>Explicit solvent trajectories</h2> <p>The following Folding@home projects were analyzed for manuscript, and are made available here as full explicit solvent trajectories:</p> <p>11414: AurA +TPX2, pdb 1OL5</p> <ul> <li>RUN0: WT</li> <li>RUN1: Q185C</li> <li>RUN2: Q185L</li> <li>RUN3: Q185M</li> <li>RUN4: Q185N</li> </ul> <p>11419: AurA +TPX2, pdb 1OL5 <em> RUN0: WT </em> RUN1: WT <em> RUN2: WT </em> RUN3: WT <em> RUN4: Q185H -- has no data, input was broken </em> RUN5: C247A * RUN6: C247L</p> <p>11418: AurA -TPX2, pdb 1OL5 <em> RUN0: WT </em> RUN1: WT <em> RUN2: WT </em> RUN3: WT * RUN4: WT</p> <p>11423: AurA -TPX2, pdb 1OL5 <em> RUN0: Q185C </em> RUN1: Q185L <em> RUN2: Q185M </em> RUN3: Q185N <em> RUN4: Q185H </em> RUN5: C247A * RUN6: C247L</p> <p>Each trajectory is available in the appropriate project folder:</p> <pre class="highlight"><code>AurA Folding@home simulations &gt; explicit solvent &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 the mutant or WT replicate 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> <h2>Processed data</h2> <p>The processed data can be found in a single archive containing <a href="https://docs.scipy.org/doc/numpy/reference/generated/numpy.save.html" rel="nofollow">numpy <code>.npy</code> archives</a> as <code>processed-data.tgz</code> under "AurA processed data".</p>
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