http://wiki.docking.org/index.php?action=history&feed=atom&title=Preparing_dockfiles_using_TLDR 2026-04-04T22:15:59Z Revision history for this page on the wiki MediaWiki 1.39.1 http://wiki.docking.org/index.php?title=Preparing_dockfiles_using_TLDR&diff=14632&oldid=prev 2022-08-09T18:43:19Z

<p><span dir="auto"><span class="autocomment">step 1. Download sample data: </span> asdf</span></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 18:43, 9 August 2022</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l7">Line 7:</td> <td colspan="2" class="diff-lineno">Line 7:</td></tr> <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>== step 2. submit jobs to TLDR</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>== step 2. submit jobs to TLDR</div></td></tr> <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;"><br/></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;"><br/></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Step 2. Prepare receptor for docking.  In general, preparing a receptor for a docking campaign requires an expert. There are simply too many permutations and combinations to offer a universal, automatic solution to the preparation of any receptor for docking. Fortunately, for some cases the preparation can be done automatically. We have therefore developed an automated approach to receptor preparation (blastermaster2.0) and made it available via a website (TLDR.docking.org) [Knight, 2022]. Even easier, for the 40 DUDEZ benchmarking targets, the receptors have been prepared in advance and may simply be downloaded.  Sample data for 40 targets are available at dudez2022.docking.org. For illustration, we will use the prepared model for the beta2 adrenergic receptor, dudez2022.docking.org/ADRB2/dockfiles.tar.gz. </ins></div></td></tr> <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;"><br/></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;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>== step 3. wait for email indicating blastermaster 2.0 is finished.  </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>== step 3. wait for email indicating blastermaster 2.0 is finished.</div></td></tr> <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;"><br/></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;"><br/></td></tr> <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>== step 4. inspect results. be sure docking is working, then use for AWS docking run ==  </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>== step 4. inspect results. be sure docking is working, then use for AWS docking run ==  </div></td></tr> <!-- diff cache key wikidb:diff::1.12:old-14626:rev-14632 --> </table>

Frodo http://wiki.docking.org/index.php?title=Preparing_dockfiles_using_TLDR&diff=14626&oldid=prev 2022-08-09T16:37:20Z

<p>asdf</p> <p><b>New page</b></p><div>This page describes how to use TLDR:blaster2.0 service to create dockfiles for large scale docking. <br /> <br /> <br /> == step 1. Download sample data ==<br /> use dudez2022.docking.org<br /> <br /> == step 2. submit jobs to TLDR<br /> <br /> <br /> == step 3. wait for email indicating blastermaster 2.0 is finished. <br /> <br /> == step 4. inspect results. be sure docking is working, then use for AWS docking run == <br /> <br /> [[Category:AWS]]<br /> [[Category:TLDR]]<br /> [[Category:docking]]</div>

Frodo