User contributions for TBalius
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4 December 2016
- 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