http://wiki.docking.org/index.php?action=history&feed=atom&title=Hackathon_2024_to_consolidate_the_standard_lab_protocol 2026-05-13T04:26:51Z Revision history for this page on the wiki MediaWiki 1.39.1 http://wiki.docking.org/index.php?title=Hackathon_2024_to_consolidate_the_standard_lab_protocol&diff=16102&oldid=prev 2024-05-25T00:33:41Z

<p>asdf</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 00:33, 25 May 2024</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l42">Line 42:</td> <td colspan="2" class="diff-lineno">Line 42:</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;"><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><del style="font-weight: bold; text-decoration: none;">*</del></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><ins style="font-weight: bold; text-decoration: none;">[[Category:Hackathon]]</ins></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><ins style="font-weight: bold; text-decoration: none;">[[Category:Protocol]]</ins></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><ins style="font-weight: bold; text-decoration: none;">[[Category:Documentation]]</ins></div></td></tr> <!-- diff cache key wikidb:diff::1.12:old-15924:rev-16102 --> </table>

Frodo http://wiki.docking.org/index.php?title=Hackathon_2024_to_consolidate_the_standard_lab_protocol&diff=15924&oldid=prev 2024-05-23T18:07:41Z

<p>asdf</p> <p><b>New page</b></p><div>The standard lab protocol has become frayed at the edges. <br /> The purpose of this hackathon is to consolidate the multiple scripts in the lab and to arrive at a new lab protocol that captures all the best practices, tips and tricks and insider knowledge.<br /> <br /> To begin, we enumerate the existing pages that need to be consolidated.<br /> <br /> https://docs.google.com/document/d/1n0MBDGq7gQ6brBE4wV8WD2MJRC6ZhSn3n9pwhXAOuGc/edit#heading=h.6k8tvj60u0k3<br /> <br /> (and references cited within) <br /> <br /> The bender paper<br /> <br /> https://docs.google.com/document/d/1BWSWjn3bEL3kcYL01syyXZGTs7eBZFOjHsnxPZsh4R4/edit<br /> <br /> Elissa&#039;s protocol<br /> <br /> https://docs.google.com/document/d/16xYvFlS1McYEd3_QfOLLsO2ukIuHRz3FNhJuh8QPzio/edit<br /> <br /> other documents?<br /> <br /> <br /> The protocols to be standardized are <br /> <br /> * set up an run a molecular docking screen on Wynton<br /> * variant 1: standard protocol (ligands and target structure(s) available)<br /> * variant 2: target structure is not obvious, further modeling/testing required<br /> * variant 3: flexible receptor docking<br /> * variant 4: GIST <br /> * variant 5: no control ligands available<br /> <br /> * build 3D database - ZINC-22 style<br /> * variant 1: build for ZINC-22 at the 10M per job scale<br /> * variant 2: build up to 1000 for standalone use<br /> * variant 3: build at the 10 million scale for standalone use<br /> <br /> * scoreopt protocols<br /> * grid visualization protocols<br /> <br /> * how to setup a new computational lab protocols<br /> <br /> * experimental lab protocols<br /> <br /> <br /> <br /> *</div>

Frodo