User contributions for TBalius
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19 April 2017
- 16:5216:52, 19 April 2017 diff hist 0 Tutorial on running DOCK3.7 with GIST →docking
- 16:5116:51, 19 April 2017 diff hist +350 Tutorial on running DOCK3.7 with GIST →prepare system for docking
18 April 2017
- 21:0021:00, 18 April 2017 diff hist +3,860 Tutorial on running DOCK3.7 with GIST →enrichment
- 17:5217:52, 18 April 2017 diff hist +5 DOCK 3.7 2015/04/15 abl1 Tutorial →set up directories and get databases
- 17:4817:48, 18 April 2017 diff hist +16 DOCK 3.7 2015/04/15 abl1 Tutorial →run enrichment calculations
- 17:3017:30, 18 April 2017 diff hist −4 Ligand preparation - 20170424 →3 ways to build ligands:
- 17:2917:29, 18 April 2017 diff hist +6 Ligand preparation - 20170424 →3 ways to build ligands:
- 17:2717:27, 18 April 2017 diff hist −4 Ligand preparation - 20170424 →3 ways to build ligands:
- 17:0917:09, 18 April 2017 diff hist +2,390 Ligand preparation - 20170424 No edit summary
- 15:5515:55, 18 April 2017 diff hist +306 Tutorial on running Molecular Dynamics for GIST grid generation with scripts →Run GIST post processing
- 15:1415:14, 18 April 2017 diff hist +288 Tutorial on running Molecular Dynamics for GIST grid generation with scripts 2 No edit summary
17 April 2017
- 23:2323:23, 17 April 2017 diff hist +6,859 Tutorial on running DOCK3.7 with GIST →docking
- 23:1823:18, 17 April 2017 diff hist 0 Tutorial on running DOCK3.7 with GIST No edit summary
- 21:5521:55, 17 April 2017 diff hist +137 DOCK 3.7 2015/04/15 abl1 Tutorial →run enrichment calculations
- 21:3721:37, 17 April 2017 diff hist +118 DOCK 3.7 2015/04/15 abl1 Tutorial →Visualize the docking spheres
- 20:3220:32, 17 April 2017 diff hist +2,551 Tutorial on running DOCK3.7 with GIST →prepare system for docking (flex)
- 19:1719:17, 17 April 2017 diff hist +3,637 Tutorial on running DOCK3.7 with GIST No edit summary
- 18:4818:48, 17 April 2017 diff hist +98 Tutorial on running Molecular Dynamics for GIST grid generation with scripts No edit summary
- 18:4618:46, 17 April 2017 diff hist +4,353 N Tutorial on running Molecular Dynamics for GIST grid generation with scripts 2 Created page with "here is 003md.tleap_reduce.csh: #!/bin/csh # This script uses first reduce and then tleap to prepare a receptor for amber. # The outputs are: parameter topology file (prm7..."
- 18:4418:44, 17 April 2017 diff hist +2 Tutorial on running Molecular Dynamics for GIST grid generation with scripts →Prepare for AMBER
- 18:4318:43, 17 April 2017 diff hist +145 Tutorial on running Molecular Dynamics for GIST grid generation with scripts →Prepare for AMBER
- 18:1318:13, 17 April 2017 diff hist +20,538 Tutorial on running Molecular Dynamics for GIST grid generation with scripts →Run GIST post processing
- 17:4717:47, 17 April 2017 diff hist +17,769 Tutorial on running Molecular Dynamics for GIST grid generation with scripts No edit summary
- 17:2417:24, 17 April 2017 diff hist +9,391 Tutorial on running Molecular Dynamics for GIST grid generation with scripts →Prepare for AMBER
- 17:0817:08, 17 April 2017 diff hist −27 Tutorial on running Molecular Dynamics for GIST grid generation with scripts →Set up directories
- 16:5916:59, 17 April 2017 diff hist +1,244 N Tutorial on running Molecular Dynamics for GIST grid generation with scripts Created page with "Tutorial written by Trent Balius (Jan. 9, 2017). Here are more GIST related tutorials: DOCK_3.7_with_GIST_tutorials == Disclaimer == This is foremost for training Shoic..."
- 16:5616:56, 17 April 2017 diff hist +83 DOCK 3.7 with GIST tutorials No edit summary
- 16:5516:55, 17 April 2017 diff hist +73 Tutorial on running DOCK3.7 with GIST No edit summary
- 16:5416:54, 17 April 2017 diff hist +72 Tutorial on running Molecular Dynamics for GIST grid generation No edit summary
14 April 2017
- 22:1022:10, 14 April 2017 diff hist +121 DOCK 3.7 2015/04/15 abl1 Tutorial →run be_blasti.py
- 21:4221:42, 14 April 2017 diff hist +136 DOCK 3.7 2015/04/15 abl1 Tutorial No edit summary
12 April 2017
- 15:2815:28, 12 April 2017 diff hist +1 Ligand preparation - 20170424 No edit summary
28 February 2017
- 00:1400:14, 28 February 2017 diff hist +64 Tutorial on running Molecular Dynamics for GIST grid generation →Prepare for AMBER
- 00:1200:12, 28 February 2017 diff hist +96 Tutorial on running Molecular Dynamics for GIST grid generation →Prepare for AMBER
- 00:0100:01, 28 February 2017 diff hist +14 Tutorial on running Molecular Dynamics for GIST grid generation No edit summary
30 January 2017
- 16:3616:36, 30 January 2017 diff hist +2 Tutorial on running DOCK3.7 with GIST No edit summary
- 16:3516:35, 30 January 2017 diff hist −5 Tutorial on running DOCK3.7 with GIST No edit summary
- 16:3516:35, 30 January 2017 diff hist +357 Tutorial on running DOCK3.7 with GIST No edit summary
- 16:2816:28, 30 January 2017 diff hist +195 N Tutorial on running DOCK3.7 with GIST Created page with " This tutorial assumes that you have already completed the MD tutorial [Tutorial on running Molecular Dynamics for GIST grid generation]. # use the align the receptor and lig..."
24 January 2017
- 18:1918:19, 24 January 2017 diff hist −79 Tutorial on running Molecular Dynamics for GIST grid generation →Run convergence analysis
- 18:1518:15, 24 January 2017 diff hist +2,704 Tutorial on running Molecular Dynamics for GIST grid generation →Run convergence analysis
- 17:4617:46, 24 January 2017 diff hist −1 Tutorial on running Molecular Dynamics for GIST grid generation →Run convergence analysis
- 17:4617:46, 24 January 2017 diff hist −154 Tutorial on running Molecular Dynamics for GIST grid generation →Run convergence analysis
- 17:4517:45, 24 January 2017 diff hist +2 Tutorial on running Molecular Dynamics for GIST grid generation →Run convergence analysis
- 17:4417:44, 24 January 2017 diff hist +330 Tutorial on running Molecular Dynamics for GIST grid generation →Run GIST post processing
- 17:1317:13, 24 January 2017 diff hist +146 Tutorial on running Molecular Dynamics for GIST grid generation →Run convergence analysis
- 17:1117:11, 24 January 2017 diff hist +1,193 Tutorial on running Molecular Dynamics for GIST grid generation →Run convergence analysis
- 17:0417:04, 24 January 2017 diff hist +84 Tutorial on running Molecular Dynamics for GIST grid generation →Combining GIST grids
- 17:0217:02, 24 January 2017 diff hist +4 Tutorial on running Molecular Dynamics for GIST grid generation →Combining GIST grids
- 17:0217:02, 24 January 2017 diff hist +1,191 Tutorial on running Molecular Dynamics for GIST grid generation →Combining GIST grids
23 January 2017
- 19:5719:57, 23 January 2017 diff hist +20 Tutorial on running Molecular Dynamics for GIST grid generation →Disclaimer
- 17:5317:53, 23 January 2017 diff hist +201 Tutorial on running Molecular Dynamics for GIST grid generation →Combining GIST grids
- 17:3317:33, 23 January 2017 diff hist +1,327 Tutorial on running Molecular Dynamics for GIST grid generation →Run GIST post processing
- 17:3017:30, 23 January 2017 diff hist −1 Tutorial on running Molecular Dynamics for GIST grid generation →Run GIST post processing
- 17:2917:29, 23 January 2017 diff hist +1,718 Tutorial on running Molecular Dynamics for GIST grid generation →Run GIST post processing
- 16:3416:34, 23 January 2017 diff hist +1 Tutorial on running Molecular Dynamics for GIST grid generation No edit summary
- 16:3316:33, 23 January 2017 diff hist −31 Tutorial on running Molecular Dynamics for GIST grid generation No edit summary
- 16:3116:31, 23 January 2017 diff hist +1,737 Tutorial on running Molecular Dynamics for GIST grid generation No edit summary
22 January 2017
- 18:3618:36, 22 January 2017 diff hist +10,057 Tutorial on running Molecular Dynamics for GIST grid generation →Run AMBER
- 02:2702:27, 22 January 2017 diff hist +41 Tutorial on running Molecular Dynamics for GIST grid generation →Run AMBER
- 02:2002:20, 22 January 2017 diff hist +1 Tutorial on running Molecular Dynamics for GIST grid generation →Prepare for AMBER
- 02:1902:19, 22 January 2017 diff hist +92 Tutorial on running Molecular Dynamics for GIST grid generation →Prepare for AMBER
- 02:1502:15, 22 January 2017 diff hist −18 Tutorial on running Molecular Dynamics for GIST grid generation →Prepare for AMBER
- 02:1202:12, 22 January 2017 diff hist +708 Tutorial on running Molecular Dynamics for GIST grid generation →Prepare for AMBER
- 01:5701:57, 22 January 2017 diff hist +1,854 Tutorial on running Molecular Dynamics for GIST grid generation →Prepare for AMBER
- 01:3401:34, 22 January 2017 diff hist +60 Tutorial on running Molecular Dynamics for GIST grid generation →Set up environment
- 01:3401:34, 22 January 2017 diff hist +78 Tutorial on running Molecular Dynamics for GIST grid generation →Prepare for AMBER
- 01:2901:29, 22 January 2017 diff hist +77 Tutorial on running Molecular Dynamics for GIST grid generation →Prepare for AMBER
- 01:2701:27, 22 January 2017 diff hist +1,496 Tutorial on running Molecular Dynamics for GIST grid generation No edit summary
20 January 2017
- 17:2117:21, 20 January 2017 diff hist +166 Tutorial on running Molecular Dynamics for GIST grid generation No edit summary
9 January 2017
- 19:4019:40, 9 January 2017 diff hist +817 N Tutorial on running Molecular Dynamics for GIST grid generation Created page with " Tutorial written by Trent Balius (Jan. 9, 2017). == Disclaimer == This is foremost for training in house Shoichet lab members. But we hope that the community finds this us..."
- 18:1918:19, 9 January 2017 diff hist +134 Chimera No edit summary current
- 18:1618:16, 9 January 2017 diff hist +1,383 N Chimera Tutorial (Delta opioid receptor) Created page with "Delta opioid receptor By Reed Stein, 2016 PSPG bootcamp at UCSF. 1. Open Chimera 2. Select an atom or residue by holding CTRL and clicking 3. Rotate the protein by clickin..."
- 18:1318:13, 9 January 2017 diff hist +27 Useful chimera commands No edit summary
- 18:1218:12, 9 January 2017 diff hist −1 Chimera Tutorial (AMPC) No edit summary current
7 January 2017
- 18:1518:15, 7 January 2017 diff hist +8 Chimera Tutorial (AMPC) No edit summary
- 18:1418:14, 7 January 2017 diff hist +41 Chimera Tutorial (AMPC) No edit summary
- 18:1118:11, 7 January 2017 diff hist +2,041 N Chimera Tutorial (AMPC) Created page with "Based on Powers & Shoichet 2002 paper on characterizing the AMPC binding site: Characterizing the β-lactamase binding site Chimera tutorial 1. Open Chimera 2. Select an at..."
- 18:0518:05, 7 January 2017 diff hist +19 Useful chimera commands →Command line
- 18:0318:03, 7 January 2017 diff hist +55 Useful chimera commands No edit summary
6 January 2017
- 22:5522:55, 6 January 2017 diff hist −2 Using thin spheres in DOCK3.7 →Tutorial for using Thin Spheres in DOCK 3.7
- 22:5422:54, 6 January 2017 diff hist +104 Using thin spheres in DOCK3.7 →Tutorial for using Thin Spheres in DOCK 3.7
- 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
23 April 2015
- 23:5723:57, 23 April 2015 diff hist +42 DOCK 3.7 2015/04/15 abl1 Tutorial →make the hing region more polar
- 23:5623:56, 23 April 2015 diff hist +1 DOCK 3.7 tart No edit summary
- 17:5017:50, 23 April 2015 diff hist 0 DOCK 3.7 2015/04/15 abl1 Tutorial →make the hing regen more polar
- 00:1600:16, 23 April 2015 diff hist +69 DOCK 3.7 2015/04/15 abl1 Tutorial No edit summary
19 April 2015
- 16:5916:59, 19 April 2015 diff hist +11 DOCK 3.7 2015/04/15 abl1 Tutorial No edit summary
- 14:1314:13, 19 April 2015 diff hist +149 DOCK 3.7 2015/04/15 abl1 Tutorial No edit summary
18 April 2015
- 00:3500:35, 18 April 2015 diff hist +3,934 DOCK 3.7 2015/04/15 abl1 Tutorial →improving docking
- 00:2400:24, 18 April 2015 diff hist 0 N File:Modspheres.png No edit summary current
- 00:2400:24, 18 April 2015 diff hist +305 DOCK 3.7 2015/04/15 abl1 Tutorial No edit summary
- 00:1700:17, 18 April 2015 diff hist +73 DOCK 3.7 2015/04/15 abl1 Tutorial →combine scores and poses
- 00:1600:16, 18 April 2015 diff hist 0 N File:Decoydock.png No edit summary current
- 00:1500:15, 18 April 2015 diff hist 0 N File:Liganddock.png No edit summary current
- 00:1400:14, 18 April 2015 diff hist −1 DOCK 3.7 2015/04/15 abl1 Tutorial →create AUC plot of ligands and decoys
17 April 2015
- 21:0621:06, 17 April 2015 diff hist +7 DOCK 3.7 2015/04/15 abl1 Tutorial →run blastermaster.py
- 21:0621:06, 17 April 2015 diff hist +187 DOCK 3.7 2015/04/15 abl1 Tutorial →combine scores and poses
- 20:4720:47, 17 April 2015 diff hist +414 DOCK 3.7 2015/04/15 abl1 Tutorial →create AUC plot of ligands and decoys
- 20:4420:44, 17 April 2015 diff hist 0 N File:AblROCplot.png No edit summary current
- 20:4420:44, 17 April 2015 diff hist +166 DOCK 3.7 2015/04/15 abl1 Tutorial →create AUC plot of ligands and decoys
- 20:4120:41, 17 April 2015 diff hist 0 N File:Spheresbox.png No edit summary current
- 20:4020:40, 17 April 2015 diff hist +255 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 20:3620:36, 17 April 2015 diff hist +22 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 20:3620:36, 17 April 2015 diff hist −2 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 20:3420:34, 17 April 2015 diff hist +94 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 20:3120:31, 17 April 2015 diff hist −2 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 20:2720:27, 17 April 2015 diff hist +3,924 DOCK 3.7 2015/04/15 abl1 Tutorial No edit summary
- 20:2020:20, 17 April 2015 diff hist +2,575 DOCK 3.7 2015/04/15 abl1 Tutorial No edit summary
- 20:1020:10, 17 April 2015 diff hist −9 DOCK 3.7 2015/04/15 abl1 Tutorial →run enrichment calucaltions
- 20:0920:09, 17 April 2015 diff hist −98 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 20:0720:07, 17 April 2015 diff hist 0 File:Spheres.png TBalius uploaded a new version of "File:Spheres.png" current
- 20:0620:06, 17 April 2015 diff hist 0 N File:Spheres.png No edit summary
- 20:0420:04, 17 April 2015 diff hist +9 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 20:0320:03, 17 April 2015 diff hist −16 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 20:0320:03, 17 April 2015 diff hist +105 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 20:0220:02, 17 April 2015 diff hist +38 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 20:0020:00, 17 April 2015 diff hist +156 DOCK 3.7 2015/04/15 abl1 Tutorial →run blastermaster.py
15 April 2015
- 22:4022:40, 15 April 2015 diff hist −12 DOCK 3.7 2015/04/15 abl1 Tutorial No edit summary
- 22:1722:17, 15 April 2015 diff hist +6 DOCK 3.7 2015/04/15 abl1 Tutorial No edit summary
- 22:0222:02, 15 April 2015 diff hist +275 DOCK 3.7 2015/04/15 abl1 Tutorial →run blastermaster.py
- 21:4621:46, 15 April 2015 diff hist −3,782 DOCK 3.7 2015/04/15 abl1 Tutorial No edit summary
- 21:4321:43, 15 April 2015 diff hist +5,528 DOCK 3.7 2015/04/15 abl1 Tutorial No edit summary
- 21:4121:41, 15 April 2015 diff hist +3,686 DOCK 3.7 2015/04/15 abl1 Tutorial →run blastermaster.py
- 21:3521:35, 15 April 2015 diff hist 0 N File:Rec lig 2HYY.png No edit summary current
- 21:3221:32, 15 April 2015 diff hist +420 DOCK 3.7 2015/04/15 abl1 Tutorial →run be_blasti.py
- 21:2521:25, 15 April 2015 diff hist +416 N Get msms Created page with " see the following website for information: [http://mgltools.scripps.edu/packages/MSMS/ msms page] ==Installing MSMS == wget http://mgltools.scripps.edu/downloads/tars/rel..."
- 21:2121:21, 15 April 2015 diff hist +2,479 DOCK 3.7 2015/04/15 abl1 Tutorial →run be_blasti.py
- 21:1121:11, 15 April 2015 diff hist −37 DOCK 3.7 2015/04/15 abl1 Tutorial No edit summary
- 21:1021:10, 15 April 2015 diff hist +101 DOCK 3.7 2015/04/15 abl1 Tutorial No edit summary
- 21:0921:09, 15 April 2015 diff hist +116 DOCK 3.7 2015/04/15 abl1 Tutorial →set up directories and get databases
- 21:0521:05, 15 April 2015 diff hist +18 DOCK 3.7 2015/04/15 abl1 Tutorial No edit summary
- 21:0421:04, 15 April 2015 diff hist +1,212 DOCK 3.7 2015/04/15 abl1 Tutorial →set up a directory
- 20:4020:40, 15 April 2015 diff hist +213 N DOCK 3.7 2015/04/15 abl1 Tutorial Created page with " This tutoral use the 3.7.2 beta version of dock release on XXX. == set up a directory == == download enrichment databases == == run be_blasti.py== == run blastermaster.py..."
- 20:3620:36, 15 April 2015 diff hist +40 DOCK 3.7 No edit summary
19 March 2015
6 March 2015
- 17:0917:09, 6 March 2015 diff hist +223 How to compile DOCK No edit summary
5 March 2015
- 19:5319:53, 5 March 2015 diff hist −5 How to compile DOCK →debuging dock
- 19:5219:52, 5 March 2015 diff hist +663 How to compile DOCK No edit summary
- 19:3619:36, 5 March 2015 diff hist +1 Install DOCK 3.7 No edit summary
23 October 2014
- 15:4615:46, 23 October 2014 diff hist +87 Mol2db2 No edit summary current
- 15:4515:45, 23 October 2014 diff hist +58 DOCK 3.7 No edit summary
- 15:4415:44, 23 October 2014 diff hist +293 Mol2db2 Format 2 No edit summary current
26 September 2014
- 17:4517:45, 26 September 2014 diff hist +65 DOCK 3.7 2014/09/25 FXa Tutorial No edit summary
- 17:4117:41, 26 September 2014 diff hist +52 N File:Veiwdock.FXa.frag.top200.png chimera veiwdock session for FXa with top 200 frags. current
- 17:3817:38, 26 September 2014 diff hist +64 DOCK 3.7 2014/09/25 FXa Tutorial →pose visualization
- 13:0613:06, 26 September 2014 diff hist +15 DOCK 3.7 2014/09/25 FXa Tutorial →Receptor Preparation
- 13:0513:05, 26 September 2014 diff hist +3 DOCK 3.7 2014/09/25 FXa Tutorial →This part of the tutorial uses the GIST development version of DOCK
- 13:0513:05, 26 September 2014 diff hist +135 DOCK 3.7 2014/09/25 FXa Tutorial →This part of the tutorial uses the GIST development version of DOCK
- 12:5612:56, 26 September 2014 diff hist +62 DOCK 3.7 2014/09/25 FXa Tutorial No edit summary
- 12:5512:55, 26 September 2014 diff hist +377 DOCK 3.7 2014/09/25 FXa Tutorial No edit summary
- 12:4912:49, 26 September 2014 diff hist +348 DOCK 3.7 2014/09/25 FXa Tutorial →Receptor Preparation