User contributions for TBalius
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28 March 2020
- 23:3723:37, 28 March 2020 diff hist +2,701 N Prepare a receptor with a cofactor for docking Created page with " This page is written by Trent E. Balius (FNLCR) on March 28, 2020. This is for cases where the cofactor does not already have cofactors. For the receptor, I use Chimera'..." current
- 23:3423:34, 28 March 2020 diff hist +53 DOCK 3.7 →Start here
24 March 2020
- 10:1010:10, 24 March 2020 diff hist +126 Useful chimera commands No edit summary current
- 10:0610:06, 24 March 2020 diff hist +579 Useful chimera commands No edit summary
26 August 2019
- 13:2913:29, 26 August 2019 diff hist 0 Minimize protein-covalent ligand complex with AMBER No edit summary current
25 March 2019
- 19:3219:32, 25 March 2019 diff hist +38 Install DOCK 3.7 →Installing third-party softwares current
6 February 2019
- 18:5118:51, 6 February 2019 diff hist +62 Calculate volume of the binding site and molecules No edit summary current
- 18:5018:50, 6 February 2019 diff hist +109 N PDB surface points for figures Created page with " Related content: *Using_thin_spheres_in_DOCK3.7 *Calculate_volume_of_the_binding_site_and_molecules" current
- 18:4918:49, 6 February 2019 diff hist +42 Other Useful Stuff No edit summary
28 January 2019
- 20:0120:01, 28 January 2019 diff hist +15 How to do parameter scanning No edit summary
26 January 2019
- 18:4118:41, 26 January 2019 diff hist +36 DOCK 3.7 →Prepare Receptor
24 January 2019
- 01:2901:29, 24 January 2019 diff hist +87 Calculate volume of the binding site and molecules →Calculating the volume of a binding site.
3 January 2019
- 19:5519:55, 3 January 2019 diff hist +3 Minimize protein-covalent ligand complex with AMBER No edit summary
- 19:4719:47, 3 January 2019 diff hist 0 Minimize protein-covalent ligand complex with AMBER No edit summary
17 December 2018
- 21:3221:32, 17 December 2018 diff hist 0 File:2018 12 coval1.png TBalius uploaded a new version of "File:2018 12 coval1.png" current
- 21:2421:24, 17 December 2018 diff hist 0 File:2018 12 coval1.png TBalius uploaded a new version of "File:2018 12 coval1.png"
- 21:1621:16, 17 December 2018 diff hist 0 File:2018 12 coval1.png TBalius uploaded a new version of "File:2018 12 coval1.png"
- 20:1720:17, 17 December 2018 diff hist 0 N File:2018 12 coval1.png No edit summary
- 19:2319:23, 17 December 2018 diff hist +270 Minimize protein-covalent ligand complex with AMBER No edit summary
- 19:1419:14, 17 December 2018 diff hist +1,302 Minimize protein-covalent ligand complex with AMBER No edit summary
- 19:1019:10, 17 December 2018 diff hist +1,278 Minimize protein-covalent ligand complex with AMBER No edit summary
- 19:0719:07, 17 December 2018 diff hist +928 Minimize protein-covalent ligand complex with AMBER No edit summary
- 19:0119:01, 17 December 2018 diff hist +8,601 Minimize protein-covalent ligand complex with AMBER No edit summary
- 17:5817:58, 17 December 2018 diff hist +76 Minimize protein-covalent ligand complex with AMBER No edit summary
- 17:5517:55, 17 December 2018 diff hist +7,998 N Minimize protein-covalent ligand complex with AMBER Created page with " This is for ligands that modify a specific residue. (1) Make a directory: mkdir coval_min cd coval_min/ (2) Download pdb file from the web: wget https://files.rcsb...."
- 17:1917:19, 17 December 2018 diff hist +58 DOCK 3.7 →Prepare Receptor
15 December 2018
- 01:3401:34, 15 December 2018 diff hist +143 Minimize protein-ligand complex with AMBER →Step 4. Run minimization using the amber program PMEMD.cuda on a GPU machine current
6 December 2018
- 21:5021:50, 6 December 2018 diff hist −4 How to cite →DOCK 6 current
- 21:4921:49, 6 December 2018 diff hist +279 How to cite No edit summary
26 September 2018
- 17:1317:13, 26 September 2018 diff hist +451 DOCK 3.7 2018/06/05 abl1 Tutorial →combining the results
- 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
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: current
- 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