User contributions for TBalius
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6 January 2017
- 22:4922:49, 6 January 2017 diff hist +229 Using thin spheres in DOCK3.7 No edit summary
- 22:3722:37, 6 January 2017 diff hist +68 Using thin spheres in DOCK3.7 →Tutorial for using Thin Spheres in DOCK 3.7
- 22:2422:24, 6 January 2017 diff hist +87 Using thin spheres in DOCK3.7 →Tutorial for using Thin Spheres in DOCK 3.7
- 22:1622:16, 6 January 2017 diff hist +42 Using thin spheres in DOCK3.7 →Tutorial for using Thin Spheres in DOCK 3.7
- 22:1522:15, 6 January 2017 diff hist +488 Using thin spheres in DOCK3.7 No edit summary
5 January 2017
- 23:4623:46, 5 January 2017 diff hist −3 DOCK 3.7 with GIST tutorials No edit summary
- 23:4323:43, 5 January 2017 diff hist +256 N DOCK 3.7 with GIST tutorials Created page with " To docking with GIST, you must generate gist grids using molecular dynamics to generate a trajectory and this post process it with cpptraj. * Tutorial on running Molecula..."
- 23:4023:40, 5 January 2017 diff hist +35 DOCK 3.7 No edit summary
14 December 2016
- 21:1921:19, 14 December 2016 diff hist 0 Using thin spheres in DOCK3.7 No edit summary
- 00:5600:56, 14 December 2016 diff hist +54 Useful chimera commands No edit summary
- 00:5400:54, 14 December 2016 diff hist −3 Using thin spheres in DOCK3.7 No edit summary
- 00:5300:53, 14 December 2016 diff hist −4 Using thin spheres in DOCK3.7 No edit summary
7 December 2016
- 01:5901:59, 7 December 2016 diff hist +20 Calculate volume of the binding site and molecules No edit summary
- 01:5801:58, 7 December 2016 diff hist +1,474 Calculate volume of the binding site and molecules No edit summary
4 December 2016
- 22:3122:31, 4 December 2016 diff hist +166 Calculate volume of the binding site and molecules No edit summary
- 22:2622:26, 4 December 2016 diff hist +681 Calculate volume of the binding site and molecules →Calculating the volume of a binding site.
- 22:1722:17, 4 December 2016 diff hist −1 Calculate volume of the binding site and molecules →how the volume calculation works.
- 22:0522:05, 4 December 2016 diff hist +51 Calculate volume of the binding site and molecules →Calculating the volume of a small molecule.
- 22:0222:02, 4 December 2016 diff hist +66 Calculate volume of the binding site and molecules No edit summary
- 22:0122:01, 4 December 2016 diff hist +298 Calculate volume of the binding site and molecules No edit summary
- 21:5721:57, 4 December 2016 diff hist +377 Calculate volume of the binding site and molecules No edit summary
- 21:5021:50, 4 December 2016 diff hist +8 Calculate volume of the binding site and molecules No edit summary
- 21:4921:49, 4 December 2016 diff hist +1,542 Calculate volume of the binding site and molecules →Calculating the volume of a small molecule.
- 21:4221:42, 4 December 2016 diff hist 0 Calculate volume of the binding site and molecules No edit summary
- 21:4221:42, 4 December 2016 diff hist +55 Calculate volume of the binding site and molecules No edit summary
- 21:3921:39, 4 December 2016 diff hist +18 Calculate volume of the binding site and molecules No edit summary
- 21:3821:38, 4 December 2016 diff hist +1,094 N Calculate volume of the binding site and molecules Created page with " Written by Trent Balius, Dec. 2016. ==The the volume calculation works.== Lay a grid over the spheres. Count the number or points contained in the spheres (Ns). Count the ..."
- 21:3321:33, 4 December 2016 diff hist +84 N Other Useful Stuff Created page with " Useful chimera commands calculate volume of the binding site and molecules"
- 21:3121:31, 4 December 2016 diff hist 0 DOCK 3.7 No edit summary
- 21:3121:31, 4 December 2016 diff hist +25 DOCK 3.7 No edit summary
2 December 2016
- 16:5216:52, 2 December 2016 diff hist +333 N Useful chimera commands Created page with " ==Command line== You might like to make a small molecules (eg. HEM) part of the surface of the protein instead of separate: surfcat one #1:1-290 surf one probeRadius 1...."
18 November 2016
- 20:2120:21, 18 November 2016 diff hist −6 ZINC15:examples:public No edit summary
3 November 2016
- 19:0519:05, 3 November 2016 diff hist +225 Using thin spheres in DOCK3.7 No edit summary
- 18:5118:51, 3 November 2016 diff hist +32 Using thin spheres in DOCK3.7 No edit summary
- 18:4918:49, 3 November 2016 diff hist −23 Using thin spheres in DOCK3.7 No edit summary
- 18:4118:41, 3 November 2016 diff hist +77 Using thin spheres in DOCK3.7 No edit summary
- 18:2518:25, 3 November 2016 diff hist +32 Using thin spheres in DOCK3.7 No edit summary
- 18:2018:20, 3 November 2016 diff hist +12 Using thin spheres in DOCK3.7 No edit summary
- 18:1718:17, 3 November 2016 diff hist +547 Using thin spheres in DOCK3.7 No edit summary
- 17:2017:20, 3 November 2016 diff hist +98 Using thin spheres in DOCK3.7 No edit summary
- 16:0716:07, 3 November 2016 diff hist +41 Using thin spheres in DOCK3.7 No edit summary
- 15:4615:46, 3 November 2016 diff hist +303 Using thin spheres in DOCK3.7 No edit summary
- 00:1000:10, 3 November 2016 diff hist +119 Using thin spheres in DOCK3.7 No edit summary
2 November 2016
- 23:4223:42, 2 November 2016 diff hist −4 Using thin spheres in DOCK3.7 No edit summary
- 22:2122:21, 2 November 2016 diff hist +991 N Using thin spheres in DOCK3.7 Created page with "1) Run blastermaster.py. this will gerenate two directorys: working and dockfiles 2) make a new directory called mk_thin_spheres: mkdir mk_thin_spheres cd mk_thin_sph..."
- 22:2122:21, 2 November 2016 diff hist −2 DOCK 3.7 tutorial (Anat) →Using modified(existing) delphi spheres:
- 22:2022:20, 2 November 2016 diff hist +36 DOCK 3.7 tutorial (Anat) No edit summary
19 September 2016
- 18:1818:18, 19 September 2016 diff hist +520 DOCK 3.7 2015/04/15 abl1 Tutorial →Modify matching spheres
- 18:0518:05, 19 September 2016 diff hist −2 DOCK 3.7 tart No edit summary
- 18:0518:05, 19 September 2016 diff hist +137 DOCK 3.7 tart No edit summary
- 02:0602:06, 19 September 2016 diff hist +58 DOCK 3.7 2015/04/15 abl1 Tutorial →run enrichment calculations
- 02:0402:04, 19 September 2016 diff hist +1 DOCK 3.7 2015/04/15 abl1 Tutorial →run enrichment calculations
- 01:5901:59, 19 September 2016 diff hist +114 DOCK 3.7 2016/09/16 Tutorial for Enrichment Calculations (Trent & Jiankun) →Submit an enrichment calculation via 0003.lig-decoy_enrichment_submit.csh current
- 01:5701:57, 19 September 2016 diff hist +279 DOCK 3.7 2016/09/16 Tutorial for Enrichment Calculations (Trent & Jiankun) No edit summary
- 01:5301:53, 19 September 2016 diff hist +846 DOCK 3.7 2015/04/15 abl1 Tutorial →run enrichment calculations
- 01:3301:33, 19 September 2016 diff hist 0 DOCK 3.7 2015/04/15 abl1 Tutorial No edit summary
- 01:2601:26, 19 September 2016 diff hist −84 DOCK 3.7 2016/09/16 Tutorial for Enrichment Calculations (Trent & Jiankun) No edit summary
16 September 2016
- 16:1916:19, 16 September 2016 diff hist +208 DOCK 3.7 2015/04/15 abl1 Tutorial →run blastermaster.py
- 16:1116:11, 16 September 2016 diff hist +410 DOCK 3.7 2015/04/15 abl1 Tutorial →create AUC plot of ligands and decoys
14 September 2016
- 19:2319:23, 14 September 2016 diff hist −6 Copying files No edit summary current
- 19:1619:16, 14 September 2016 diff hist +223 Copying files No edit summary
23 May 2016
- 17:0917:09, 23 May 2016 diff hist +516 INDOCK 3.7 No edit summary
26 April 2016
- 23:4623:46, 26 April 2016 diff hist +1,332 N Rescoring with DOCK 3.7 Created page with " We often want to get the score for a molecule without doing any docking. DOCK3.7 now can do this internally. In DOCK 3.6 this was done in an exteranl program scoreopt. =..."
- 23:3723:37, 26 April 2016 diff hist +29 DOCK 3.7 2014/09/25 FXa Tutorial →This part of the tutorial uses the GIST development version of DOCK current
8 April 2016
- 18:0118:01, 8 April 2016 diff hist +177 Install DOCK 3.7 No edit summary
7 April 2016
- 17:2317:23, 7 April 2016 diff hist +116 DOCK 3.7 2015/04/15 abl1 Tutorial →curating and hit-picking
- 17:0817:08, 7 April 2016 diff hist +200 DOCK 3.7 2015/04/15 abl1 Tutorial →submitting the docking calculations
- 17:0517:05, 7 April 2016 diff hist +254 DOCK 3.7 2015/04/15 abl1 Tutorial →combining the results
- 16:2516:25, 7 April 2016 diff hist +40 DOCK 3.7 2015/04/15 abl1 Tutorial →submitting the docking calculations
- 16:2416:24, 7 April 2016 diff hist +867 DOCK 3.7 2015/04/15 abl1 Tutorial →database setup
6 April 2016
- 21:2621:26, 6 April 2016 diff hist +249 AMSOL No edit summary
- 20:0420:04, 6 April 2016 diff hist +41 DOCK 3.7 tutorial (Anat) →ligand prep
- 20:0220:02, 6 April 2016 diff hist −2 DOCK 3.7 tutorial (Anat) →ligand prep
5 April 2016
- 15:2615:26, 5 April 2016 diff hist +93 History of DOCK 6 →Version 3.5 current
26 January 2016
- 16:5116:51, 26 January 2016 diff hist +42 DOCK 3.7 tutorial (Anat) →Using modified(existing) matching spheres:
- 16:4816:48, 26 January 2016 diff hist +539 DOCK 3.7 tutorial (Anat) No edit summary
25 January 2016
- 19:4019:40, 25 January 2016 diff hist +443 DOCK 3.7 tutorial (Anat) No edit summary
12 October 2015
- 18:0118:01, 12 October 2015 diff hist +7 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 17:5617:56, 12 October 2015 diff hist 0 DOCK 3.7 2015/04/15 abl1 Tutorial No edit summary
- 17:5117:51, 12 October 2015 diff hist +260 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
2 October 2015
- 22:1022:10, 2 October 2015 diff hist +1 ZINC15:update policy No edit summary
11 September 2015
- 21:2621:26, 11 September 2015 diff hist +73 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 21:0921:09, 11 September 2015 diff hist +2 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 21:0921:09, 11 September 2015 diff hist +84 DOCK 3.7 2015/04/15 abl1 Tutorial No edit summary
15 July 2015
- 21:2221:22, 15 July 2015 diff hist +110 How to compile DOCK →profiling dock
29 June 2015
- 17:2417:24, 29 June 2015 diff hist +40 DOCK 3.7 tutorial (Anat) No edit summary
- 17:2117:21, 29 June 2015 diff hist +101 DOCK 3.7 tutorial (Anat) No edit summary
25 June 2015
- 22:4522:45, 25 June 2015 diff hist +5,169 N DOCK 3.7 tutorial (Anat) Created page with "==DOCK 3.7== source /nfs/soft/dock/DOCK-3.7-beta3/env.csh source ~/.cshrc_dock37 (my home directory) *“Up directory” refers to the main directory that contains the ‘doc..."
- 22:3522:35, 25 June 2015 diff hist +31 DOCK 3.7 →Start here
18 June 2015
- 16:2216:22, 18 June 2015 diff hist +142 Trent scripts No edit summary current
29 May 2015
- 18:2218:22, 29 May 2015 diff hist +25 Install DOCK 3.7 No edit summary
- 18:2018:20, 29 May 2015 diff hist +102 Amsol 7 patch No edit summary current
- 15:5415:54, 29 May 2015 diff hist +96 N Amsol 7 patch Created page with " The Amsol 7 patch is located here: $DOCKBASE/ligand/amsol/patches/amsol7.1_port_intcar.f.diff"
12 May 2015
- 22:3622:36, 12 May 2015 diff hist +1,463 DOCKovalent 3.7 →Sending a run
- 21:1721:17, 12 May 2015 diff hist +42 DOCKovalent 3.7 →INDOCK parameters
- 19:2219:22, 12 May 2015 diff hist −12 DOCKovalent 3.7 →Sending a run
- 18:4518:45, 12 May 2015 diff hist +406 DOCKovalent 3.7 →General setup
- 18:3418:34, 12 May 2015 diff hist +143 DOCKovalent 3.7 →General setup
- 18:3118:31, 12 May 2015 diff hist +167 DOCKovalent 3.7 →General setup