http://wiki.docking.org/index.php?action=history&feed=atom&title=Good_ligand_pose 2026-04-09T12:05:19Z Revision history for this page on the wiki MediaWiki 1.39.1 http://wiki.docking.org/index.php?title=Good_ligand_pose&diff=2892&oldid=prev 2012-10-08T20:25:24Z

<p>2 revisions</p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <tr class="diff-title" lang="en"> <td colspan="1" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="1" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:25, 8 October 2012</td> </tr><tr><td colspan="2" class="diff-notice" lang="en"><div class="mw-diff-empty">(No difference)</div> </td></tr></table>

Therese http://wiki.docking.org/index.php?title=Good_ligand_pose&diff=2891&oldid=prev 2007-09-20T21:18:41Z

<p></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 21:18, 20 September 2007</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l20">Line 20:</td> <td colspan="2" class="diff-lineno">Line 20:</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>* bad tautomer or protonation choice</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>* bad tautomer or protonation choice</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>* broken molecule</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>* broken molecule</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 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 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:DOCK]]</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:Opinion]]</ins></div></td></tr> </table>

JohnIrwin http://wiki.docking.org/index.php?title=Good_ligand_pose&diff=2890&oldid=prev 2007-09-13T01:35:44Z

<p></p> <p><b>New page</b></p><div>What makes a good ligand pose? You can see for yourself by examinging the experimentally observed poses of ligands in the [[protein data bank]] (aka PDB).<br /> <br /> When reviewing hits from a docking screen, here are the features we look for: <br /> <br /> == good features ==<br /> * overall good shape complementarity<br /> * good polar matches between ligand and protein<br /> * good apolar matches between ligand and protein<br /> * not too floppy<br /> <br /> == bad features ==<br /> * dangle polarity into solvent (bad because part of the ligand is being &quot;wasted&quot;)<br /> * polar to apolar matchups between ligand and protein<br /> * failure to use features of ligand or protein in binding site<br /> * too floppy<br /> <br /> == problems specific to dock3.5.54 (and thus DOCK Blaster) ==<br /> <br /> * bad conformation (&quot;internal clashes&quot;)<br /> * bad tautomer or protonation choice<br /> * broken molecule</div>

JohnIrwin