User contributions for TBalius
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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
14 February 2018
- 19:2419:24, 14 February 2018 diff hist +193 Enm explorer No edit summary current
2 February 2018
- 16:1616:16, 2 February 2018 diff hist +433 Enm explorer No edit summary
31 January 2018
- 20:1720:17, 31 January 2018 diff hist +50 How to process results from a large-scale docking →Cluster results
- 19:5619:56, 31 January 2018 diff hist +98 Enm explorer No edit summary
- 01:2501:25, 31 January 2018 diff hist +103 How to process results from a large-scale docking →Combine results
- 01:2401:24, 31 January 2018 diff hist +116 How to process results from a large-scale docking →Cluster results
29 November 2017
- 18:5018:50, 29 November 2017 diff hist +351 Rescoring with DOCK 3.7 →how to generate need files
- 18:3618:36, 29 November 2017 diff hist +201 Rescoring with DOCK 3.7 →how to generate need files
- 18:2718:27, 29 November 2017 diff hist +4,212 Rescoring with DOCK 3.7 →how to generate need files
17 November 2017
- 22:5322:53, 17 November 2017 diff hist −1 Ligand preparation - 20170424 →3 ways to build ligands:
- 19:3919:39, 17 November 2017 diff hist +4 Tutorial on running DOCK3.7 with blury-GIST No edit summary current
- 19:3819:38, 17 November 2017 diff hist +521 Tutorial on running DOCK3.7 with blury-GIST No edit summary
16 November 2017
- 16:4316:43, 16 November 2017 diff hist +2 Tutorial on running DOCK3.7 with blury-GIST No edit summary
- 01:3101:31, 16 November 2017 diff hist +138 Tutorial on running DOCK3.7 with GIST →Prepare system for docking current
- 01:3001:30, 16 November 2017 diff hist +133 Tutorial on running DOCK3.7 with GIST →Get ligand databases
15 November 2017
- 20:0920:09, 15 November 2017 diff hist +247 N Tutorial on running DOCK3.7 with blury-GIST Created page with " Use the following python script to blur GIST grids: GIST_DX_tools/src/dx-gist_precalculate_sphere_gausian.py infile sphradius divider pad_radius outfileprefix Note the ..."
- 19:5619:56, 15 November 2017 diff hist +50 DOCK 3.7 with GIST tutorials No edit summary current
- 00:1900:19, 15 November 2017 diff hist +42 DOCK3.7 INDOCK Minimization Parameter →Information on number_save and number_write parameters current
- 00:1800:18, 15 November 2017 diff hist +57 DOCK3.7 INDOCK Minimization Parameter →Information on number_save and number_write parameters
- 00:0600:06, 15 November 2017 diff hist 0 File:Miminizer.2017.11.14.png TBalius uploaded a new version of "File:Miminizer.2017.11.14.png" current