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DOCK 3.5 - Revision history
2024-03-29T05:15:20Z
Revision history for this page on the wiki
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http://wiki.docking.org/index.php?title=DOCK_3.5&diff=11410&oldid=prev
Khtang at 21:44, 10 January 2019
2019-01-10T21:44:56Z
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Khtang
http://wiki.docking.org/index.php?title=DOCK_3.5&diff=11409&oldid=prev
Khtang at 21:43, 10 January 2019
2019-01-10T21:43:48Z
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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>''DOCK 3.5 is no longer available''. A substantial modification of DOCK 3.5, now called [[DOCK 3.6]], continues to be used, maintained, and distributed by the [[Shoichet Laboratory]].</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>''DOCK 3.5 is no longer available''. A substantial modification of DOCK 3.5, now called [[DOCK 3.6]], continues to be used, maintained, and distributed by the [[Shoichet Laboratory]].<ins style="font-weight: bold; text-decoration: none;"></br></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>DOCK 3.5, released in 1993-4, superceded [[DOCK 3]] and all previous versions of [[DOCK]]. It was written in Fortran 77.</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>DOCK 3.5, released in 1993-4, superceded [[DOCK 3]] and all previous versions of [[DOCK]]. It was written in Fortran 77.</div></td></tr>
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Khtang
http://wiki.docking.org/index.php?title=DOCK_3.5&diff=11408&oldid=prev
Khtang at 21:43, 10 January 2019
2019-01-10T21:43:26Z
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 21:43, 10 January 2019</td>
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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>DOCK 3.5, released in 1993-4, superceded [[DOCK 3]] and all previous versions of [[DOCK]]. It was written in Fortran 77. DOCK <del style="font-weight: bold; text-decoration: none;">3</del>.5 is no <del style="font-weight: bold; text-decoration: none;">longer available</del>. <del style="font-weight: bold; text-decoration: none;">A substantial modification </del>of DOCK <del style="font-weight: bold; text-decoration: none;">3</del>.<del style="font-weight: bold; text-decoration: none;">5</del>, <del style="font-weight: bold; text-decoration: none;">now called </del>[[<del style="font-weight: bold; text-decoration: none;">DOCK 3</del>.<del style="font-weight: bold; text-decoration: none;">6</del>]]<del style="font-weight: bold; text-decoration: none;">, continues </del>to be used, <del style="font-weight: bold; text-decoration: none;">maintained</del>, and <del style="font-weight: bold; text-decoration: none;">distributed </del>by the [[<del style="font-weight: bold; text-decoration: none;">Shoichet Laboratory]</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;">''DOCK 3.5 is no longer available''. A substantial modification of DOCK 3.5, now called [[DOCK 3.6]], continues to be used, maintained, and distributed by the [[Shoichet Laboratory]].</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>DOCK 3.5, released in 1993-4, superceded [[DOCK 3]] and all previous versions of [[DOCK]]. It was written in Fortran 77.</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><ins style="font-weight: bold; text-decoration: none;">==General operation changes to DOCK3.5==</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><ins style="font-weight: bold; text-decoration: none;">• Everything that happens after the generation of a rotation-matrix has been completely re-written. This includes applying the rotation-matrix, scoring the atoms, sorting to get the hit list, saving the hit list, and writing output. The way ligands are read in has also been re-written.</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><ins style="font-weight: bold; text-decoration: none;">• Northwestern DOCK accepts the name of an INDOCK file as argument on the command line. If no argument is provided, INDOCK is assumed.</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><ins style="font-weight: bold; text-decoration: none;">• Northwestern </ins>DOCK <ins style="font-weight: bold; text-decoration: none;">saves the atom coordinates for molecules in the hit list instead of the rotation-matrices needed to regenerate the orientation. This was initially done to avoid the time-consuming process of re-reading the database to get the best molecules. An additional benefit to this method is that at any time during the run, the best molecules can easily be visualized.</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><ins style="font-weight: bold; text-decoration: none;">• Focusing has been removed as implemented in DOCK3.5 and re-implemented based on Brian’s work with DOCK2</ins>.5<ins style="font-weight: bold; text-decoration: none;">. Coloring with focusing has not been thoroughly tested but seems to work.</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><ins style="font-weight: bold; text-decoration: none;">• Every conformation and every orientation of small molecule ligands [Shoichet, Leach, & Kuntz 1999] and mutated protein-ligand resides can be completely desolvated at essentially no computational cost.</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><ins style="font-weight: bold; text-decoration: none;">• Currently the only valid scoring option in Northwestern DOCK </ins>is <ins style="font-weight: bold; text-decoration: none;">5. This uses the CHEMGRID generated van der Waals grid, DISTMAP generated contact grid, and a DelPhi generated electrostatics grid of dimensions 65×65×65. Re-implementing CHEMGRID electrostatics should be trivial.</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><ins style="font-weight: bold; text-decoration: none;">Simplex Minimization: Three values are accepted for the minimize parameter. </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;">• None (or </ins>no<ins style="font-weight: bold; text-decoration: none;">) -- does no energy minimization, is fast, and frequently produces qualitatively correct hit lists. My tests suggest that while minimizing produces better scoring molecules that make more hydrogen bonds than their non-minimized counterparts, minimizing does not significantly change the types of molecules populating the hit lists.</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><ins style="font-weight: bold; text-decoration: none;">• Best (or rigid or yes) -- evaluates only the best conformation at each vertex of the simplex minimizer and continues only evaluating this single conformation through all steps of minimization. This is significantly slower (order of magnitude) than not minimizing</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><ins style="font-weight: bold; text-decoration: none;">• Hierarchy -- evaluates the entire hierarchy for each vertex of the simplex minimizer and continues to re-evaluate the hierarchy at each step </ins>of <ins style="font-weight: bold; text-decoration: none;">minimization. This allows the conformation to change as the minimization proceeds. This option is the slowest.</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><ins style="font-weight: bold; text-decoration: none;">Degeneracy checking: The following degeneracy checking keywords must be removed for Northwestern </ins>DOCK <ins style="font-weight: bold; text-decoration: none;">to function: degeneracy_wobble, degenerate_save_interval, check_degenerate_children. The current degeneracy checking routine, if turned on, only removes orientations generated from repeated spheres. Degeneracy checking currently does not significantly improve results or significantly reduce run-time. I recommend that degeneracy checking be turned off (i.e</ins>., <ins style="font-weight: bold; text-decoration: none;">check_degeneracy no).</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;">New/Modified keywords:</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><ins style="font-weight: bold; text-decoration: none;">bump_max </ins>[<ins style="font-weight: bold; text-decoration: none;">integer] -- This keyword describes the number of ligand bumps allowed per branch. The definition of this keyword was changed because determining the total number of bumps per molecule is time consuming if reliably implemented in a recombination-docking scheme.</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><ins style="font-weight: bold; text-decoration: none;">focus_bump </ins>[<ins style="font-weight: bold; text-decoration: none;">integer] -- Maximum number of bumps (per branch) allowed in an orientation to allow focusing to occur. The implementation of focusing is a modified version of that found in DOCK2</ins>.<ins style="font-weight: bold; text-decoration: none;">5 (Shoichet, 1992)</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;">focus_type [shape or energy</ins>] <ins style="font-weight: bold; text-decoration: none;">-- If focusing is turned on, additional spheres will be used to find similar orientations. For the first round of focusing, all orientations under focus_bump are further refined. For all subsequent rounds, only the best scoring orientation will be used for additional focusing. The best orientation is either the highest contact score or lowest energy score.</ins></div></td></tr>
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<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;">ligand_desolvation [residue, full, or none</ins>] <ins style="font-weight: bold; text-decoration: none;">-- This keyword is for the type of ligand desolvation </ins>to be used<ins style="font-weight: bold; text-decoration: none;">. Currently accepted values are: full (subtract the entire ligand desolvation value), residue (subtract the pre-calculated, hard-coded value for 25 amino acid variations), or none (no desolvation). Only full and residue are currently implemented. Only residues that are in contact with the receptor are desolvated when using residue desolvation. In the future I anticipate this keyword will also have the value ‘partial’</ins>, <ins style="font-weight: bold; text-decoration: none;">and possibly a counterpart keyword receptor_desolvation.</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><ins style="font-weight: bold; text-decoration: none;">minimization_max [real value] -- The value for this parameter is the maximum, pre-minimized energy score that will be minimized. This is used primarily to speed calculations when focusing and minimizing are being used together – focus to get low energy structures</ins>, and <ins style="font-weight: bold; text-decoration: none;">then minimize.</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;">recombine_fragments [yes or no] -- This option allows for recombining fragments from different molecules within a family to generate an overall best scoring molecule. This option is supported by dock (tested with proteins), but the current database is not organized </ins>by <ins style="font-weight: bold; text-decoration: none;">family so this option has no effect.</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><ins style="font-weight: bold; text-decoration: none;">split_database_index -- This is a special value for the ligand_atom_file keyword. If this value is used, </ins>the <ins style="font-weight: bold; text-decoration: none;">filename is read as a plain-text file. Each line of split_database_index should have a complete path to the database files to be used.</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><ins style="font-weight: bold; text-decoration: none;">timeout </ins>[<ins style="font-weight: bold; text-decoration: none;">real value] -- Maximum time in seconds allowed per molecule. The default is 86400 (one day in seconds). It is possible that some molecules may take an inordinate amount of time to dock. This is particularly important for molecules containing a large number of rotors in a single branch that contains downstream sub-branches. We find setting this value to 120 seconds is a good compromise. Molecules that timeout will be reported as timing out in the OUTDOCK file. (Added by John Irwin, modified by DL)</ins></div></td></tr>
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<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;">truncate_output </ins>[<ins style="font-weight: bold; text-decoration: none;">real value</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;">This parameter is read only in single mode docking. The value for this parameter is the maximum RMS from the starting point to the docked orientation that will have coordinates written out</ins>. <ins style="font-weight: bold; text-decoration: none;"> RMS values greater than truncate_output will have only remark lines written out</ins></div></td></tr>
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Khtang
http://wiki.docking.org/index.php?title=DOCK_3.5&diff=564&oldid=prev
Therese: 2 revisions
2012-10-08T20:02:00Z
<p>2 revisions</p>
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Therese
http://wiki.docking.org/index.php?title=DOCK_3.5&diff=563&oldid=prev
Frodo at 19:27, 11 May 2011
2011-05-11T19:27:31Z
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 19:27, 11 May 2011</td>
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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>DOCK 3.5, released in 1993-4, superceded DOCK 3 and all previous versions of DOCK. It was written in Fortran 77. DOCK 3.5 is no longer available. <del style="font-weight: bold; text-decoration: none;">However, a </del>substantial modification of DOCK 3.5, called [[DOCK 3.<del style="font-weight: bold; text-decoration: none;">5.54</del>]], continues to be used, maintained, and distributed. </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>DOCK 3.5, released in 1993-4, superceded <ins style="font-weight: bold; text-decoration: none;">[[</ins>DOCK 3<ins style="font-weight: bold; text-decoration: none;">]] </ins>and all previous versions of <ins style="font-weight: bold; text-decoration: none;">[[</ins>DOCK<ins style="font-weight: bold; text-decoration: none;">]]</ins>. It was written in Fortran 77. DOCK 3.5 is no longer available. <ins style="font-weight: bold; text-decoration: none;">A </ins>substantial modification of DOCK 3.5, <ins style="font-weight: bold; text-decoration: none;">now </ins>called [[DOCK 3.<ins style="font-weight: bold; text-decoration: none;">6</ins>]], continues to be used, maintained, and distributed <ins style="font-weight: bold; text-decoration: none;">by the [[Shoichet Laboratory]]</ins>.</div></td></tr>
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Frodo
http://wiki.docking.org/index.php?title=DOCK_3.5&diff=562&oldid=prev
JohnIrwin at 07:45, 30 November 2007
2007-11-30T07:45:17Z
<p></p>
<p><b>New page</b></p><div>DOCK 3.5, released in 1993-4, superceded DOCK 3 and all previous versions of DOCK. It was written in Fortran 77. DOCK 3.5 is no longer available. However, a substantial modification of DOCK 3.5, called [[DOCK 3.5.54]], continues to be used, maintained, and distributed. <br />
<br />
[[Category:DOCK]]</div>
JohnIrwin