User contributions for TBalius
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26 September 2018
- 15:4515:45, 26 September 2018 diff hist +970 Rescoring with DOCK 3.7 No edit summary current
14 September 2018
- 18:2818:28, 14 September 2018 diff hist −9 Calculate volume of the binding site and molecules No edit summary
- 18:2618:26, 14 September 2018 diff hist −2 Calculate volume of the binding site and molecules No edit summary
- 18:2618:26, 14 September 2018 diff hist +130 Calculate volume of the binding site and molecules No edit summary
31 July 2018
- 18:0218:02, 31 July 2018 diff hist −3 Using thin spheres in DOCK3.7 →Tutorial for using Thin Spheres in DOCK 3.7.1rc1
20 July 2018
- 17:1217:12, 20 July 2018 diff hist +53 Sample Additional Ring Puckers No edit summary current
- 16:1416:14, 20 July 2018 diff hist −11 Sample Additional Ring Puckers No edit summary
- 16:0016:00, 20 July 2018 diff hist −3 Sample Additional Ring Puckers →new script in developmental version (DOCKBASE = ~tbalius/zzz.github/DOCK)
- 15:5015:50, 20 July 2018 diff hist +1,163 Sample Additional Ring Puckers No edit summary
21 June 2018
- 17:5717:57, 21 June 2018 diff hist +211 Sample Additional Ring Puckers No edit summary
- 17:4817:48, 21 June 2018 diff hist +38 Sample Additional Ring Puckers No edit summary
- 17:4517:45, 21 June 2018 diff hist +270 Sample Additional Ring Puckers No edit summary
- 17:1917:19, 21 June 2018 diff hist 0 Sample Additional Ring Puckers No edit summary
- 17:1917:19, 21 June 2018 diff hist +133 Sample Additional Ring Puckers No edit summary
- 16:0816:08, 21 June 2018 diff hist +43 DOCK 3.7 No edit summary
- 16:0116:01, 21 June 2018 diff hist +36 Sample Additional Ring Puckers No edit summary
- 15:5315:53, 21 June 2018 diff hist +1,162 N Sample Additional Ring Puckers Created page with " 1. create a directory and cd into it mkdir ZINC000001664886 cd ZINC000001664886 2. copy the protonated smiles into the current directory cp ../../normal_db2_gen/isom..."
20 June 2018
- 15:5215:52, 20 June 2018 diff hist +74 DOCK 3.7 No edit summary
12 June 2018
- 00:4500:45, 12 June 2018 diff hist +31 DOCK 3.7 2018/06/05 abl1 Tutorial →run blastermaster.py
- 00:4400:44, 12 June 2018 diff hist +575 DOCK 3.7 2018/06/05 abl1 Tutorial →run blastermaster.py
7 June 2018
- 22:5722:57, 7 June 2018 diff hist +182 Whole Library TC to Knowns Calculations No edit summary
- 22:1622:16, 7 June 2018 diff hist −5 Whole Library TC to Knowns Calculations No edit summary
5 June 2018
- 15:5915:59, 5 June 2018 diff hist −2,629 DOCK 3.7 2018/06/05 abl1 Tutorial →run enrichment calculations
- 15:5615:56, 5 June 2018 diff hist 0 DOCK 3.7 2015/04/15 abl1 Tutorial No edit summary
- 15:5615:56, 5 June 2018 diff hist +75 DOCK 3.7 2015/04/15 abl1 Tutorial No edit summary
- 15:5415:54, 5 June 2018 diff hist +28,855 N DOCK 3.7 2018/06/05 abl1 Tutorial Created page with " This tutorial use the 3.7.2 beta version of dock release on April 17, 2015. This is for a Linux environment and the scripts assume that you are running on SGE queuing system..."
- 15:5315:53, 5 June 2018 diff hist +51 DOCK 3.7 →Start here
4 June 2018
- 17:1517:15, 4 June 2018 diff hist +224 DOCK 3.7 2015/04/15 abl1 Tutorial →Modify matching spheres
2 May 2018
- 21:5021:50, 2 May 2018 diff hist +300 DOCK 3.7 2015/04/15 abl1 Tutorial →combine scores and poses
16 April 2018
- 22:4222:42, 16 April 2018 diff hist +54 Ssh tunnel (Trent's way) No edit summary
- 22:3922:39, 16 April 2018 diff hist +192 Ssh tunnel (Trent's way) No edit summary
- 22:3222:32, 16 April 2018 diff hist +100 Ssh tunnel (Trent's way) No edit summary
- 22:3122:31, 16 April 2018 diff hist −21 Ssh tunnel (Trent's way) No edit summary
- 22:3022:30, 16 April 2018 diff hist +1,183 N Ssh tunnel (Trent's way) Created page with " (1) Open two terminals. In the first terminal write one of the following lines: ssh -CL 2222:gimel.ucsf.bkslab.org:22 -D1080 tbalius@portal.ucsf.bkslab.org -p 22 -i ~/.ssh..."
- 20:5420:54, 16 April 2018 diff hist +45 Minimize protein-ligand complex with AMBER →Step 2. Prepare ligand charges and force field.
- 17:5917:59, 16 April 2018 diff hist +31 Welcome group members →Access from home
12 April 2018
- 16:4516:45, 12 April 2018 diff hist +5 Using thin spheres in DOCK3.7 →Tutorial for using Thin Spheres in DOCK 3.7
- 16:4316:43, 12 April 2018 diff hist +2,085 Using thin spheres in DOCK3.7 No edit summary
11 April 2018
- 17:5317:53, 11 April 2018 diff hist +200 Using thin spheres in DOCK3.7 No edit summary
6 April 2018
- 20:1620:16, 6 April 2018 diff hist −2 Minimize protein-ligand complex with AMBER →Step 2. Prepare ligand charges and force field.
- 20:0920:09, 6 April 2018 diff hist +431 Minimize protein-ligand complex with AMBER →Step 2. Prepare ligand charges and force field.
- 00:4700:47, 6 April 2018 diff hist +1 Minimize protein-ligand complex with AMBER →Step 4. Run minimization using the amber program PMEMD.cuda on a GPU machine
- 00:4700:47, 6 April 2018 diff hist +1 Minimize protein-ligand complex with AMBER →Step 4. Run minimization using the amber program PMEMD.cuda on a GPU machine
- 00:4700:47, 6 April 2018 diff hist +27 Minimize protein-ligand complex with AMBER →Step 4. Run minimization using the amber program PMEMD.cuda on a GPU machine
- 00:4000:40, 6 April 2018 diff hist +325 Minimize protein-ligand complex with AMBER →Step 4. Run minimization using the amber program PMEMD.cuda on a GPU machine
2 April 2018
- 17:1917:19, 2 April 2018 diff hist +65 Minimize protein-ligand complex with AMBER No edit summary
- 17:1817:18, 2 April 2018 diff hist −6 Minimize protein-ligand complex with AMBER No edit summary
- 17:1717:17, 2 April 2018 diff hist +81 Minimize protein-ligand complex with AMBER →Step 1. Break up the complex into ligand (small molecule) and receptor.
- 17:0817:08, 2 April 2018 diff hist +5,906 N Minimize protein-ligand complex with AMBER Created page with " Written on 2018/04/02 This tutorial is for Shoichet Lab group members but we hope that it might be useful to the community. Outlined below are five steps to minimize a com..."
- 16:3016:30, 2 April 2018 diff hist +49 DOCK 3.7 →Prepare Receptor