http://wiki.docking.org/index.php?action=history&feed=atom&title=DUMM2
DUMM2 - Revision history
2026-04-11T00:31:49Z
Revision history for this page on the wiki
MediaWiki 1.39.1
http://wiki.docking.org/index.php?title=DUMM2&diff=1224&oldid=prev
Therese: 20 revisions
2012-10-08T20:11:51Z
<p>20 revisions</p>
<p><b>New page</b></p><div>== Attendees & Time==<br />
# John Irwin<br />
# Sarah Boyce<br />
# Peter Kolb<br />
# Rafaela Ferreira<br />
# Alessandro Nascimento<br />
# Denise Teotico<br />
# Gabe Rocklin<br />
# Oliv Eidam<br />
# Hao Fan<br />
# Francesco Colizzi<br />
<br />
Date: July 09, 2008, 4:00pm-5:20pm<br />
<br />
'''Next DUM on August 06, 2008 at 4pm'''<br />
<br />
== Hardware updates==<br />
<br />
== Software updates ==<br />
=== getrandom.pl ===<br />
''John:'' getrandom.pl program (and website) to select molecules randomly from ZINC. If run directly, this program should be executed on korn or any other machine that has access to ZINC.<br />
<br />
===rebuildit2.pl===<br />
''John:'' rebuildit2.pl to rebuild pre-cavitation ZINC entries. This is being hooked behind DOCK Blaster, upload, and subset web services.<br />
<br />
===Requests/Improvements===<br />
<br />
== Database updates ==<br />
''John:'' recently completed ZINC8 release, including a full export of many subsets.<br />
<br />
''John:'' loaded lab molecules L99A binders, non-binders, etc. Still in beta - i.e. must be reviewed carefully. <br />
<br />
''John:'' a database of natural products is available from the ZINC web site. 90K natural products or derivatives of natural products that are commercially available.<br />
<br />
== Varia ==<br />
<br />
===Flexible receptor docking===<br />
<br />
''Sarah'' reported on how to use receptor flexibility with DOCK.<br />
<br />
===HEI database generation===<br />
<br />
''Peter'' talked about the ways to [[How to generate a HEI database|generate a database of high energy intermediates]] (HEIs).<br />
<br />
== Action Items ==<br />
<br />
<br />
[[Category:DUMM]]<br />
<br />
&rarr; back to [[Dock Users' Meeting Minutes (DUMM)|DUMM main page]]</div>
Therese
http://wiki.docking.org/index.php?title=DUMM2&diff=1217&oldid=prev
Frodo at 03:56, 10 July 2008
2008-07-10T03:56:41Z
<p></p>
<p><b>New page</b></p><div>== Attendees & Time==<br />
# John Irwin<br />
# Sarah Boyce<br />
# Peter Kolb<br />
# Rafaela Ferreira<br />
# Alessandro Nascimento<br />
# Denise Teotico<br />
# Gabe Rocklin<br />
# Oliv Eidam<br />
# Hao Fan<br />
# Francesco Colizzi<br />
<br />
Date: July 09, 2008, 4:00pm-5:20pm<br />
<br />
'''Next DUM on August 06, 2008 at 4pm'''<br />
<br />
== Hardware updates==<br />
<br />
== Software updates ==<br />
=== getrandom.pl ===<br />
''John:'' getrandom.pl program (and website) to select molecules randomly from ZINC.<br />
<br />
===rebuildit2.pl===<br />
''John:'' rebuildit2.pl to rebuild pre-cavitation ZINC entries. This is being hooked behind DOCK Blaster, upload, and subset web services.<br />
<br />
== Database updates ==<br />
''John:'' recently completed ZINC8 release, including a full export of many subsets.<br />
<br />
''John:'' loaded lab molecules L99A binders, non-binders, etc. Still in beta - i.e. must be reviewed carefully. <br />
<br />
''John:'' a database of natural products is available from the ZINC web site. 90K natural products or derivatives of natural products that are commercially available.<br />
<br />
===Requests/Improvements===<br />
<br />
== Varia ==<br />
<br />
<br />
== Action Items ==<br />
<br />
<br />
[[Category:DUMM]]<br />
<br />
back to [[Dock_Users%27_Meeting_Minutes_%28DUMM%29]]</div>
Frodo
http://wiki.docking.org/index.php?title=DUMM2&diff=1209&oldid=prev
Frodo: /* Database updates */
2008-07-09T19:07:16Z
<p><span dir="auto"><span class="autocomment">Database updates</span></span></p>
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<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 19:07, 9 July 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l17">Line 17:</td>
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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>== Database updates ==</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>== Database updates ==</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;"><div>''John:'' recently completed ZINC8 release, including a full export of many subsets.</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>''John:'' recently completed ZINC8 release, including a full export of many subsets.</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;"></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;"><div>''John:'' loaded lab molecules L99A binders, non-binders, etc. Still in beta - i.e. must be reviewed carefully. </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>''John:'' loaded lab molecules L99A binders, non-binders, etc. Still in beta - i.e. must be reviewed carefully. </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;"></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;"><div>''John:'' a database of natural products is available from the ZINC web site. 90K natural products or derivatives of natural products that are commercially available.</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>''John:'' a database of natural products is available from the ZINC web site. 90K natural products or derivatives of natural products that are commercially available.</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>===Requests/Improvements===</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>===Requests/Improvements===</div></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 colspan="2" class="diff-side-added"></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>== Varia ==</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>== Varia ==</div></td></tr>
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Frodo
http://wiki.docking.org/index.php?title=DUMM2&diff=1208&oldid=prev
Frodo at 19:06, 9 July 2008
2008-07-09T19:06:53Z
<p></p>
<p><b>New page</b></p><div>== Attendees & Time==<br />
# John Irwin<br />
# Sarah Boyce<br />
# Peter Kolb<br />
# ...<br />
<br />
Date: July 09, 2008<br />
<br />
'''Next DUM on ???'''<br />
<br />
== Hardware updates==<br />
<br />
== Software updates ==<br />
''John:'' getrandom.pl program (and website) to select molecules randomly from ZINC.<br />
''John:'' rebuildit2.pl to rebuild pre-cavitation ZINC entries. This is being hooked behind DOCK Blaster, upload, and subset web services.<br />
<br />
== Database updates ==<br />
''John:'' recently completed ZINC8 release, including a full export of many subsets.<br />
''John:'' loaded lab molecules L99A binders, non-binders, etc. Still in beta - i.e. must be reviewed carefully. <br />
''John:'' a database of natural products is available from the ZINC web site. 90K natural products or derivatives of natural products that are commercially available.<br />
<br />
===Requests/Improvements===<br />
<br />
<br />
== Varia ==<br />
<br />
<br />
== Action Items ==</div>
Frodo
http://wiki.docking.org/index.php?title=DUMM2&diff=1205&oldid=prev
Frodo at 19:03, 9 July 2008
2008-07-09T19:03:00Z
<p></p>
<p><b>New page</b></p><div>== Attendees & Time==<br />
1. John Irwin<br />
<br />
Date: July 09, 2008<br />
<br />
'''Next DUM on ???'''<br />
<br />
== Hardware updates==<br />
<br />
==Software updates==<br />
<br />
<br />
===Requests/Improvements===<br />
<br />
<br />
== Varia ==<br />
<br />
<br />
== Action Items ==</div>
Frodo