http://wiki.docking.org/index.php?title=Generate_Model&feed=atom&action=historyGenerate Model - Revision history2024-03-28T08:29:51ZRevision history for this page on the wikiMediaWiki 1.39.1http://wiki.docking.org/index.php?title=Generate_Model&diff=5903&oldid=prevFrodo at 05:09, 14 February 20142014-02-14T05:09:35Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> [prompt]$ sea-fit -c cutoff model.out</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> [prompt]$ sea-fit -c cutoff model.out</div></td></tr>
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</table>Frodohttp://wiki.docking.org/index.php?title=Generate_Model&diff=5123&oldid=prevFrodo: Created page with "This is intended for Shoichet lab setup. But we hope other find it useful. See SEA == How to generate a model to run SEA == We need the files: reference.smi ; referenc..."2012-10-11T23:14:04Z<p>Created page with "This is intended for Shoichet lab setup. But we hope other find it useful. See <a href="/index.php?title=SEA" class="mw-redirect" title="SEA">SEA</a> == How to generate a model to run SEA == We need the files: reference.smi ; referenc..."</p>
<p><b>New page</b></p><div>This is intended for Shoichet lab setup. But we hope other find it useful. See [[SEA]]<br />
<br />
== How to generate a model to run SEA ==<br />
<br />
We need the files: reference.smi ; reference.set ; reference.fp<br />
<br />
First we need to generate the background Z-score distribution:<br />
<br />
[prompt]$ sea-background reference.set.gz<br />
<br />
This generated the file model.out<br />
<br />
Then we need to fit data the data from this background model and build a fit parameter file:<br />
<br />
[prompt]$ sea-fit model.out<br />
<br />
This generates the file model.out.distfit, containing the values for the best fit of the background distribution to a normal and an extreme value distribution. From this distribution, we need to select the optimal cutoff (in general we look for the similarity value that better fits to EVD) and then use it to get the fit file.<br />
<br />
[prompt]$ sea-fit -c cutoff model.out</div>Frodo