http://wiki.docking.org/index.php?action=history&feed=atom&title=Contact_Score 2026-04-05T07:20:50Z Revision history for this page on the wiki MediaWiki 1.39.1 http://wiki.docking.org/index.php?title=Contact_Score&diff=476&oldid=prev 2012-10-08T18:10:32Z

<p>2 revisions</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 18:10, 8 October 2012</td> </tr> <!-- diff cache key wikidb:diff::1.12:old-475:rev-476 --> </table>

Therese http://wiki.docking.org/index.php?title=Contact_Score&diff=475&oldid=prev 2007-09-20T21:22:17Z

<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 21:22, 20 September 2007</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l25">Line 25:</td> <td colspan="2" class="diff-lineno">Line 25:</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>             #The prefix to the grid files containing the desired contact</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>             #The prefix to the grid files containing the desired contact</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>             #grid</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>             #grid</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:Scoring problem]]</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> </table>

JohnIrwin http://wiki.docking.org/index.php?title=Contact_Score&diff=474&oldid=prev 2006-09-19T22:52:48Z

<p></p> <p><b>New page</b></p><div>The contact score is a simple summation of the number of heavy atom contacts between the ligand and receptor. At the time of construction of the contact scoring grid, the distance threshold defining a contact is set with the contact_cutoff_distance (see Grid). Atom VDW overlaps are penalized by checking the bump filter grid, or with the contact_clash_overlap parameter for the intramolecular score. The amount of penalty is specified with the contact_clash_penalty parameter.<br /> <br /> The contact score provides a simple assessment of shape complementarity. It can be useful for evaluating primarily non-polar interactions.<br /> <br /> NOTE: The following parameter definitions will use the format below:<br /> <br /> parameter_name [default] (value):<br /> #description<br /> <br /> In some cases, parameters are only needed (questions will only be asked) if the parameter above is enforced. These parameters are indicated below by additional indentation.<br /> <br /> Contact Score Parameters<br /> <br /> * contact_score_primary [no] (yes, no):<br /> #Flag to perform contact scoring as the primary scoring function<br /> * contact_score_secondary [no] (yes, no):<br /> #Flag to perform contact scoring as the secondary scoring function<br /> o contact_score_cutoff_distance [4.5] (float):<br /> #The distance threshold defining a contact<br /> o contact_score_clash_overlap [0.75] (float):<br /> #Contact definition for use with intramolecular scoring<br /> o contact_score_clash_penalty [50] (float):<br /> #The penalty for each contact overlap made<br /> o contact_score_grid_prefix [grid] (string):<br /> #The prefix to the grid files containing the desired contact<br /> #grid</div>

JohnIrwin