http://wiki.docking.org/index.php?action=history&feed=atom&title=Decoy_TheoryDecoy Theory - Revision history2026-04-09T04:08:29ZRevision history for this page on the wikiMediaWiki 1.39.1http://wiki.docking.org/index.php?title=Decoy_Theory&diff=11287&oldid=prevKhtang: /* What are decoys? */2019-01-03T23:39:29Z<p><span dir="auto"><span class="autocomment">What are decoys?</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:39, 3 January 2019</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>*Random Decoys: A set of random molecules, usually chosen from [[ZINC]], most of which won't be binders simply by chance.</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>*Random Decoys: A set of random molecules, usually chosen from [[ZINC]], most of which won't be binders simply by chance.</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>Now, once you have these various sets, you can examine the enrichment of various sets, usually by looking at a ROC curve, log ROC curve, or the [LogAUC] of one set over the others. The most common usage is ligands over property-matched decoys. If your target does well at this, the general attitude is that you will do well at a prospective virtual screen. If you have many known decoys or known non-binders you can examine the enrichment of those over ligands, which also tends to indicate how well you are doing. Sometimes it is also illustrative to test the enrichment of ligands over random decoys (usually something like the leadlike ZINC subset, trimmed at 60% Tanimoto overlap <ref>[http://zinc.docking.org/subset1/]</ref>. A final thing to examine if you have known decoys is to examine their enrichment over random decoys, expecting random performance.</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>Now, once you have these various sets, you can examine the enrichment of various sets, usually by looking at a ROC curve, log ROC curve, or the <ins style="font-weight: bold; text-decoration: none;">[</ins>[LogAUC<ins style="font-weight: bold; text-decoration: none;">]</ins>] of one set over the others. The most common usage is ligands over property-matched decoys. If your target does well at this, the general attitude is that you will do well at a prospective virtual screen. If you have many known decoys or known non-binders you can examine the enrichment of those over ligands, which also tends to indicate how well you are doing. Sometimes it is also illustrative to test the enrichment of ligands over random decoys (usually something like the leadlike ZINC subset, trimmed at 60% Tanimoto overlap <ref>[http://zinc.docking.org/subset1/]</ref>. A final thing to examine if you have known decoys is to examine their enrichment over random decoys, expecting random performance.</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>== References ==</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>== References ==</div></td></tr>
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</table>Khtanghttp://wiki.docking.org/index.php?title=Decoy_Theory&diff=11286&oldid=prevKhtang: /* What are decoys? */2019-01-03T23:38:14Z<p><span dir="auto"><span class="autocomment">What are decoys?</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:38, 3 January 2019</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>*Random Decoys: A set of random molecules, usually chosen from [[ZINC]], most of which won't be binders simply by chance.</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>*Random Decoys: A set of random molecules, usually chosen from [[ZINC]], most of which won't be binders simply by chance.</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>Now, once you have these various sets, you can examine the enrichment of various sets, usually by looking at a ROC curve, log ROC curve, or the [LogAUC] of one set over the others. The most common usage is ligands over property-matched decoys. If your target does well at this, the general attitude is that you will do well at a prospective virtual screen. If you have many known decoys or known non-binders you can examine the enrichment of those over ligands, which also tends to indicate how well you are doing. Sometimes it is also illustrative to test the enrichment of ligands over random decoys (usually something like the leadlike ZINC subset, trimmed at 60% Tanimoto overlap <del style="font-weight: bold; text-decoration: none;">[</del>[http://zinc.docking.org/subset1/]<del style="font-weight: bold; text-decoration: none;">]</del>. A final thing to examine if you have known decoys is to examine their enrichment over random decoys, expecting random performance.</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>Now, once you have these various sets, you can examine the enrichment of various sets, usually by looking at a ROC curve, log ROC curve, or the [LogAUC] of one set over the others. The most common usage is ligands over property-matched decoys. If your target does well at this, the general attitude is that you will do well at a prospective virtual screen. If you have many known decoys or known non-binders you can examine the enrichment of those over ligands, which also tends to indicate how well you are doing. Sometimes it is also illustrative to test the enrichment of ligands over random decoys (usually something like the leadlike ZINC subset, trimmed at 60% Tanimoto overlap <ins style="font-weight: bold; text-decoration: none;"><ref></ins>[http://zinc.docking.org/subset1/]<ins style="font-weight: bold; text-decoration: none;"></ref></ins>. A final thing to examine if you have known decoys is to examine their enrichment over random decoys, expecting random performance.</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>== References ==</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>== References ==</div></td></tr>
</table>Khtanghttp://wiki.docking.org/index.php?title=Decoy_Theory&diff=11285&oldid=prevKhtang at 23:37, 3 January 20192019-01-03T23:37:28Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:37, 3 January 2019</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>*Known Decoys/ Known non-binders: A set of molecules that have been tested against your protein target and found not to bind. ChEMBL or the literature is also a source of these.</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>*Known Decoys/ Known non-binders: A set of molecules that have been tested against your protein target and found not to bind. ChEMBL or the literature is also a source of these.</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>*Property-Matched Decoys: A set of molecules, typically from [[ZINC]], that look like your ligands in chemical and physical property, but are not similar to the ligands by Tanimoto of a 2D fingerprint. Making these is explained here [[Automated_Database_Preparation#Automatic_Decoy_Generation]] and more information can be found in the Huang et al <ref>[http://pubs.acs.org/doi/abs/10.1021/jm0608356 Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem. 2006 Nov 16; 49(23):6789-801.]</ref> or Verdonk et al</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>*Property-Matched Decoys: A set of molecules, typically from [[ZINC]], that look like your ligands in chemical and physical property, but are not similar to the ligands by Tanimoto of a 2D fingerprint. Making these is explained here [[Automated_Database_Preparation#Automatic_Decoy_Generation]] and more information can be found in the Huang et al <ref>[http://pubs.acs.org/doi/abs/10.1021/jm0608356 Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem. 2006 Nov 16; 49(23):6789-801.]</ref> </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><ref>[<del style="font-weight: bold; text-decoration: none;">http</del>://pubs.acs.org/doi/full/10.1021/ci034289q Marcel L. Verdonk, Valerio Berdini,Michael J. Hartshorn,Wijnand T. M. Mooij,Christopher W. Murray,Richard D. Taylor<del style="font-weight: bold; text-decoration: none;">, and</del>, and Paul Watson</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>or Verdonk et al <ref>[<ins style="font-weight: bold; text-decoration: none;">https</ins>://pubs.acs.org/doi/full/10.1021/ci034289q Marcel L. Verdonk<ins style="font-weight: bold; text-decoration: none;">*</ins>, Valerio Berdini, Michael J. Hartshorn, Wijnand T. M. Mooij, Christopher W. Murray, Richard D. Taylor, and Paul Watson. J. <ins style="font-weight: bold; text-decoration: none;">Chem</ins>. <ins style="font-weight: bold; text-decoration: none;">Inf</ins>. <ins style="font-weight: bold; text-decoration: none;">Comput</ins>. <ins style="font-weight: bold; text-decoration: none;">Sci</ins>., <ins style="font-weight: bold; text-decoration: none;">2004</ins>, 44 (3), <ins style="font-weight: bold; text-decoration: none;">pp 793–806</ins>.]</ref> papers.</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;">Journal of Chemical Information and Computer Sciences 2004 44 (3), 793-806.]</ref></del></div></td><td colspan="2" class="diff-side-added"></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> </div></td><td colspan="2" class="diff-side-added"></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;"><ref>[http://pubs.acs</del>.<del style="font-weight: bold; text-decoration: none;">org/doi/full/10.1021/ci034289q Marcel L. Verdonk, Valerio Berdini,Michael </del>J. <del style="font-weight: bold; text-decoration: none;">Hartshorn,Wijnand T</del>. <del style="font-weight: bold; text-decoration: none;">M</del>. <del style="font-weight: bold; text-decoration: none;">Mooij,Christopher W</del>. <del style="font-weight: bold; text-decoration: none;">Murray,Richard D</del>. <del style="font-weight: bold; text-decoration: none;">Taylor</del>, <del style="font-weight: bold; text-decoration: none;">and</del>, <del style="font-weight: bold; text-decoration: none;">and Paul Watson</del></div></td><td colspan="2" class="diff-side-added"></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;">Journal of Chemical Information and Computer Sciences 2004 </del>44 (3), <del style="font-weight: bold; text-decoration: none;">793-806</del>.]</ref> papers.</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>*Random Decoys: A set of random molecules, usually chosen from [[ZINC]], most of which won't be binders simply by chance.</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>*Random Decoys: A set of random molecules, usually chosen from [[ZINC]], most of which won't be binders simply by chance.</div></td></tr>
</table>Khtanghttp://wiki.docking.org/index.php?title=Decoy_Theory&diff=11284&oldid=prevKhtang at 23:34, 3 January 20192019-01-03T23:34:14Z<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>*Known Decoys/ Known non-binders: A set of molecules that have been tested against your protein target and found not to bind. ChEMBL or the literature is also a source of these.</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>*Known Decoys/ Known non-binders: A set of molecules that have been tested against your protein target and found not to bind. ChEMBL or the literature is also a source of these.</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>*Property-Matched Decoys: A set of molecules, typically from [[ZINC]], that look like your ligands in chemical and physical property, but are not similar to the ligands by Tanimoto of a 2D fingerprint. Making these is explained here [[Automated_Database_Preparation#Automatic_Decoy_Generation]] and more information can be found in the Huang et al <ref>[http://pubs.acs.org/doi/abs/10.1021/jm0608356 Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem. 2006 Nov 16; 49(23):6789-801.]</ref> or Verdonk et al <ref>[http://pubs.acs.org/doi/full/10.1021/ci034289q Marcel L. Verdonk, Valerio Berdini,Michael J. Hartshorn,Wijnand T. M. Mooij,Christopher W. Murray,Richard D. Taylor, and, and Paul Watson</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>*Property-Matched Decoys: A set of molecules, typically from [[ZINC]], that look like your ligands in chemical and physical property, but are not similar to the ligands by Tanimoto of a 2D fingerprint. Making these is explained here [[Automated_Database_Preparation#Automatic_Decoy_Generation]] and more information can be found in the Huang et al <ref>[http://pubs.acs.org/doi/abs/10.1021/jm0608356 Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem. 2006 Nov 16; 49(23):6789-801.]</ref> or Verdonk et al</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;"><ref>[http://pubs.acs.org/doi/full/10.1021/ci034289q Marcel L. Verdonk, Valerio Berdini,Michael J. Hartshorn,Wijnand T. M. Mooij,Christopher W. Murray,Richard D. Taylor, and, and Paul Watson</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;">Journal of Chemical Information and Computer Sciences 2004 44 (3), 793-806.]</ref></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> </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><ref>[http://pubs.acs.org/doi/full/10.1021/ci034289q Marcel L. Verdonk, Valerio Berdini,Michael J. Hartshorn,Wijnand T. M. Mooij,Christopher W. Murray,Richard D. Taylor, and, and Paul Watson</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>Journal of Chemical Information and Computer Sciences 2004 44 (3), 793-806.]</ref> papers.</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>Journal of Chemical Information and Computer Sciences 2004 44 (3), 793-806.]</ref> papers.</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>
</table>Khtanghttp://wiki.docking.org/index.php?title=Decoy_Theory&diff=11283&oldid=prevKhtang at 23:33, 3 January 20192019-01-03T23:33:02Z<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;"><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>*Property-Matched Decoys: A set of molecules, typically from [[ZINC]], that look like your ligands in chemical and physical property, but are not similar to the ligands by Tanimoto of a 2D fingerprint. Making these is explained here [[Automated_Database_Preparation#Automatic_Decoy_Generation]] and more information can be found in the Huang et al <ref>[http://pubs.acs.org/doi/abs/10.1021/jm0608356 Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem. 2006 Nov 16; 49(23):6789-801.]</ref> or Verdonk et al <ref>[http://pubs.acs.org/doi/full/10.1021/ci034289q Marcel L. Verdonk, Valerio Berdini,Michael J. Hartshorn,Wijnand T. M. Mooij,Christopher W. Murray,Richard D. Taylor, and, and Paul Watson</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>*Property-Matched Decoys: A set of molecules, typically from [[ZINC]], that look like your ligands in chemical and physical property, but are not similar to the ligands by Tanimoto of a 2D fingerprint. Making these is explained here [[Automated_Database_Preparation#Automatic_Decoy_Generation]] and more information can be found in the Huang et al <ref>[http://pubs.acs.org/doi/abs/10.1021/jm0608356 Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem. 2006 Nov 16; 49(23):6789-801.]</ref> or Verdonk et al <ref>[http://pubs.acs.org/doi/full/10.1021/ci034289q Marcel L. Verdonk, Valerio Berdini,Michael J. Hartshorn,Wijnand T. M. Mooij,Christopher W. Murray,Richard D. Taylor, and, and Paul Watson</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>Journal of Chemical Information and Computer Sciences 2004 44 (3), 793-806]</ref> papers <del style="font-weight: bold; text-decoration: none;">listed below</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>Journal of Chemical Information and Computer Sciences 2004 44 (3), 793-806<ins style="font-weight: bold; text-decoration: none;">.</ins>]</ref> papers.</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>*Random Decoys: A set of random molecules, usually chosen from [[ZINC]], most of which won't be binders simply by chance.</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>*Random Decoys: A set of random molecules, usually chosen from [[ZINC]], most of which won't be binders simply by chance.</div></td></tr>
</table>Khtanghttp://wiki.docking.org/index.php?title=Decoy_Theory&diff=11282&oldid=prevKhtang at 23:30, 3 January 20192019-01-03T23:30:41Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:30, 3 January 2019</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>*Known Decoys/ Known non-binders: A set of molecules that have been tested against your protein target and found not to bind. ChEMBL or the literature is also a source of these.</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>*Known Decoys/ Known non-binders: A set of molecules that have been tested against your protein target and found not to bind. ChEMBL or the literature is also a source of these.</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>*Property-Matched Decoys: A set of molecules, typically from [[ZINC]], that look like your ligands in chemical and physical property, but are not similar to the ligands by Tanimoto of a 2D fingerprint. Making these is explained here [[Automated_Database_Preparation#Automatic_Decoy_Generation]] and more information can be found in the Huang et al <ref>[<del style="font-weight: bold; text-decoration: none;">https</del>://pubs.acs.org/doi/abs/10.1021/jm0608356 Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem. 2006 Nov 16; 49(23):6789-801.]</ref> or Verdonk et al <ref>[http://pubs.acs.org/doi/full/10.1021/ci034289q Marcel L. Verdonk<del style="font-weight: bold; text-decoration: none;">,*</del>, Valerio Berdini,Michael J. Hartshorn,Wijnand T. M. Mooij,Christopher W. Murray,Richard D. Taylor, and, and Paul Watson</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>*Property-Matched Decoys: A set of molecules, typically from [[ZINC]], that look like your ligands in chemical and physical property, but are not similar to the ligands by Tanimoto of a 2D fingerprint. Making these is explained here [[Automated_Database_Preparation#Automatic_Decoy_Generation]] and more information can be found in the Huang et al <ref>[<ins style="font-weight: bold; text-decoration: none;">http</ins>://pubs.acs.org/doi/abs/10.1021/jm0608356 Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem. 2006 Nov 16; 49(23):6789-801.]</ref> or Verdonk et al <ref>[http://pubs.acs.org/doi/full/10.1021/ci034289q Marcel L. Verdonk, Valerio Berdini,Michael J. Hartshorn,Wijnand T. M. Mooij,Christopher W. Murray,Richard D. Taylor, and, and Paul Watson</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>Journal of Chemical Information and Computer Sciences 2004 44 (3), 793-806]</ref> papers listed below.</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>Journal of Chemical Information and Computer Sciences 2004 44 (3), 793-806]</ref> papers listed below.</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>
</table>Khtanghttp://wiki.docking.org/index.php?title=Decoy_Theory&diff=11281&oldid=prevKhtang at 23:29, 3 January 20192019-01-03T23:29:55Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:29, 3 January 2019</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>*Known Decoys/ Known non-binders: A set of molecules that have been tested against your protein target and found not to bind. ChEMBL or the literature is also a source of these.</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>*Known Decoys/ Known non-binders: A set of molecules that have been tested against your protein target and found not to bind. ChEMBL or the literature is also a source of these.</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>*Property-Matched Decoys: A set of molecules, typically from [[ZINC]], that look like your ligands in chemical and physical property, but are not similar to the ligands by Tanimoto of a 2D fingerprint. Making these is explained here [[Automated_Database_Preparation#Automatic_Decoy_Generation]] and more information can be found in the Huang et al<ref>[https://pubs.acs.org/doi/abs/10.1021/jm0608356 Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem. 2006 Nov 16; 49(23):6789-801.]</ref> or Verdonk et al<ref>[Marcel L. Verdonk,*, Valerio Berdini,Michael J. Hartshorn,Wijnand T. M. Mooij,Christopher W. Murray,Richard D. Taylor, and, and Paul Watson</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>*Property-Matched Decoys: A set of molecules, typically from [[ZINC]], that look like your ligands in chemical and physical property, but are not similar to the ligands by Tanimoto of a 2D fingerprint. Making these is explained here [[Automated_Database_Preparation#Automatic_Decoy_Generation]] and more information can be found in the Huang et al <ref>[https://pubs.acs.org/doi/abs/10.1021/jm0608356 Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem. 2006 Nov 16; 49(23):6789-801.]</ref> or Verdonk et al <ref>[<ins style="font-weight: bold; text-decoration: none;">http://pubs.acs.org/doi/full/10.1021/ci034289q </ins>Marcel L. Verdonk,*, Valerio Berdini,Michael J. Hartshorn,Wijnand T. M. Mooij,Christopher W. Murray,Richard D. Taylor, and, and Paul Watson</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>Journal of Chemical Information and Computer Sciences 2004 44 (3), 793-806 <del style="font-weight: bold; text-decoration: none;">https://pubs.acs.org/doi/full/10.1021/ci034289q</del>]</ref> papers listed below.</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>Journal of Chemical Information and Computer Sciences 2004 44 (3), 793-806]</ref> papers listed below.</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>*Random Decoys: A set of random molecules, usually chosen from [[ZINC]], most of which won't be binders simply by chance.</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>*Random Decoys: A set of random molecules, usually chosen from [[ZINC]], most of which won't be binders simply by chance.</div></td></tr>
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</table>Khtanghttp://wiki.docking.org/index.php?title=Decoy_Theory&diff=11280&oldid=prevKhtang at 23:29, 3 January 20192019-01-03T23:29:01Z<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>*Known Decoys/ Known non-binders: A set of molecules that have been tested against your protein target and found not to bind. ChEMBL or the literature is also a source of these.</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>*Known Decoys/ Known non-binders: A set of molecules that have been tested against your protein target and found not to bind. ChEMBL or the literature is also a source of these.</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>*Property-Matched Decoys: A set of molecules, typically from [[ZINC]], that look like your ligands in chemical and physical property, but are not similar to the ligands by Tanimoto of a 2D fingerprint. Making these is explained here [[Automated_Database_Preparation#Automatic_Decoy_Generation]] and more information can be found in the Huang et al or Verdonk et al papers listed below.</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>*Property-Matched Decoys: A set of molecules, typically from [[ZINC]], that look like your ligands in chemical and physical property, but are not similar to the ligands by Tanimoto of a 2D fingerprint. Making these is explained here [[Automated_Database_Preparation#Automatic_Decoy_Generation]] and more information can be found in the Huang et al<ins style="font-weight: bold; text-decoration: none;"><ref>[https://pubs.acs.org/doi/abs/10.1021/jm0608356 Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem. 2006 Nov 16; 49(23):6789-801.]</ref> </ins>or Verdonk et al<ins style="font-weight: bold; text-decoration: none;"><ref>[Marcel L. Verdonk,*, Valerio Berdini,Michael J. Hartshorn,Wijnand T. M. Mooij,Christopher W. Murray,Richard D. Taylor, and, and Paul Watson</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;">Journal of Chemical Information and Computer Sciences 2004 44 (3), 793-806 https://pubs.acs.org/doi/full/10.1021/ci034289q]</ref> </ins>papers listed below.</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>*Random Decoys: A set of random molecules, usually chosen from [[ZINC]], most of which won't be binders simply by chance.</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>*Random Decoys: A set of random molecules, usually chosen from [[ZINC]], most of which won't be binders simply by chance.</div></td></tr>
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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>== References ==</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>== References ==</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> </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;"><references </ins>/<ins style="font-weight: bold; text-decoration: none;">></ins></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;">Huang, Irwin & Shoichet. [http:</del>/<del style="font-weight: bold; text-decoration: none;">/dx.doi.org/10.1021/jm0608356].</del></div></td><td colspan="2" class="diff-side-added"></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> </div></td><td colspan="2" class="diff-side-added"></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;">Verdonk et al [http://pubs.acs.org/doi/full/10.1021/ci034289q]</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>== More relevant pages ==</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>== More relevant pages ==</div></td></tr>
</table>Khtanghttp://wiki.docking.org/index.php?title=Decoy_Theory&diff=11279&oldid=prevKhtang: /* What are decoys? */2019-01-03T23:21:15Z<p><span dir="auto"><span class="autocomment">What are decoys?</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:21, 3 January 2019</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>"Decoys" is essentially a codename for a way of evaluating how well your docking program has done on a target (or a set of targets). Decoys refers to a set of molecules that (probably) won't bind to your target. Here are some terms:</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>"Decoys" is essentially a codename for a way of evaluating how well your docking program has done on a target (or a set of targets). Decoys refers to a set of molecules that (probably) won't bind to your target. Here are some terms:</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>*[[Ligands]]: A set of known ligands that bind to your protein target. Often taken from papers or a database like <del style="font-weight: bold; text-decoration: none;">ChEMBL </del>[<del style="font-weight: bold; text-decoration: none;">https</del>://www.ebi.ac.uk/chembldb/]</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>*[[Ligands]]: A set of known ligands that bind to your protein target. Often taken from papers or a database like [<ins style="font-weight: bold; text-decoration: none;">http</ins>://www.ebi.ac.uk/chembldb/ <ins style="font-weight: bold; text-decoration: none;">ChEMBL</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"></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>*Known Decoys/ Known non-binders: A set of molecules that have been tested against your protein target and found not to bind. ChEMBL or the literature is also a source of these.</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>*Known Decoys/ Known non-binders: A set of molecules that have been tested against your protein target and found not to bind. ChEMBL or the literature is also a source of these.</div></td></tr>
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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>*Random Decoys: A set of random molecules, usually chosen from [[ZINC]], most of which won't be binders simply by chance.</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>*Random Decoys: A set of random molecules, usually chosen from [[ZINC]], most of which won't be binders simply by chance.</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>Now, once you have these various sets, you can examine the enrichment of various sets, usually by looking at a ROC curve, log ROC curve, or the [LogAUC] of one set over the others. The most common usage is ligands over property-matched decoys. If your target does well at this, the general attitude is that you will do well at a prospective virtual screen. If you have many known decoys or known non-binders you can examine the enrichment of those over ligands, which also tends to indicate how well you are doing. Sometimes it is also illustrative to test the enrichment of ligands over random decoys (usually something like the leadlike ZINC subset, trimmed at 60% Tanimoto overlap [[http://zinc.docking.org/subset1/]]. A final thing to examine if you have known decoys is to examine their enrichment over random decoys, expecting random performance. </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>Now, once you have these various sets, you can examine the enrichment of various sets, usually by looking at a ROC curve, log ROC curve, or the [LogAUC] of one set over the others. The most common usage is ligands over property-matched decoys. If your target does well at this, the general attitude is that you will do well at a prospective virtual screen. If you have many known decoys or known non-binders you can examine the enrichment of those over ligands, which also tends to indicate how well you are doing. Sometimes it is also illustrative to test the enrichment of ligands over random decoys (usually something like the leadlike ZINC subset, trimmed at 60% Tanimoto overlap [[http://zinc.docking.org/subset1/]]. A final thing to examine if you have known decoys is to examine their enrichment over random decoys, expecting random performance.</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>== References ==</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>== References ==</div></td></tr>
</table>Khtanghttp://wiki.docking.org/index.php?title=Decoy_Theory&diff=6462&oldid=prevFrodo at 01:04, 11 March 20142014-03-11T01:04:29Z<p></p>
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<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>[[Category:DOCK]] [[Category:Theory]] [[Category:DUD]] [[Category:DUDE]] [[Category:Decoys]]</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>[[Category:DOCK]]</div></td></tr>
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</table>Frodo