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
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:
- 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
14 November 2017
- 23:4923:49, 14 November 2017 diff hist 0 N File:Miminizer.2017.11.14.png No edit summary
- 23:4823:48, 14 November 2017 diff hist +138 DOCK3.7 INDOCK Minimization Parameter →Information on number_save and number_write parameters
- 19:2819:28, 14 November 2017 diff hist +977 DOCK3.7 INDOCK Minimization Parameter No edit summary
10 November 2017
- 23:4923:49, 10 November 2017 diff hist +32 INDOCK 3.7 No edit summary current
- 22:5722:57, 10 November 2017 diff hist +116 DOCK 3.7 →Running Docking
9 November 2017
- 00:1800:18, 9 November 2017 diff hist +1 Tutorial on running Molecular Dynamics for GIST grid generation with scripts No edit summary current
8 November 2017
- 20:0320:03, 8 November 2017 diff hist +98 How to process results from a large-scale docking →Check for completion and resubmit failed jobs
- 20:0020:00, 8 November 2017 diff hist +126 How to process results from a large-scale docking →Check for completion and resubmit failed jobs
18 October 2017
- 22:2822:28, 18 October 2017 diff hist +186 How to process results from a large-scale docking No edit summary
- 22:2522:25, 18 October 2017 diff hist +4 How to process results from a large-scale docking No edit summary
- 22:2422:24, 18 October 2017 diff hist +92 How to process results from a large-scale docking No edit summary
- 21:3021:30, 18 October 2017 diff hist +81 How to process results from a large-scale docking →Check for completion and resubmit failed jobs
- 21:2821:28, 18 October 2017 diff hist +93 How to process results from a large-scale docking →Check for completion and resubmit failed jobs
5 October 2017
- 18:0918:09, 5 October 2017 diff hist 0 Ligand preparation - 20170424 →3 ways to build ligands:
- 18:0918:09, 5 October 2017 diff hist +69 Ligand preparation - 20170424 →3 ways to build ligands:
3 October 2017
- 15:3115:31, 3 October 2017 diff hist −1 DOCK 3.7 tutorial based on Webinar 2017/06/28 →Scenario 2: current
- 15:2915:29, 3 October 2017 diff hist −2 DOCK 3.7 tutorial based on Webinar 2017/06/28 →Scenario 2:
- 15:2915:29, 3 October 2017 diff hist +5 DOCK 3.7 tutorial based on Webinar 2017/06/28 →Scenario 2:
- 15:2815:28, 3 October 2017 diff hist +36 DOCK 3.7 tutorial based on Webinar 2017/06/28 →Scenario 2:
- 15:2515:25, 3 October 2017 diff hist +127 DOCK 3.7 tutorial based on Webinar 2017/06/28 →Scenario 2:
- 15:2015:20, 3 October 2017 diff hist +154 DOCK 3.7 tutorial based on Webinar 2017/06/28 →Scenario 2:
2 October 2017
- 16:1616:16, 2 October 2017 diff hist −1 Chimera Tutorial (Delta opioid receptor) No edit summary
29 September 2017
- 18:2618:26, 29 September 2017 diff hist +1 Using thin spheres in DOCK3.7 No edit summary
13 September 2017
- 23:1623:16, 13 September 2017 diff hist −1 ECFP4 Best First Clustering No edit summary
6 July 2017
- 17:4817:48, 6 July 2017 diff hist +40 Mailing address for the Shoichet lab No edit summary current
- 17:4217:42, 6 July 2017 diff hist +18 Mailing address for the Shoichet lab No edit summary
- 17:4117:41, 6 July 2017 diff hist +87 Mailing address for the Shoichet lab No edit summary
- 17:3617:36, 6 July 2017 diff hist +503 N Mailing address for the Shoichet lab Created page with " There are two mailing address for the Shoichet lab: (1) If you are shipping something though USPS use the following address: Name of Person 1700 4th Street Box 2550 S..."
30 June 2017
- 16:0516:05, 30 June 2017 diff hist +82 DOCK 3.7 tutorial based on Webinar 2017/06/28 No edit summary
29 June 2017
- 18:3218:32, 29 June 2017 diff hist +458 DOCK 3.7 tutorial based on Webinar 2017/06/28 →Scenario 2:
- 18:3218:32, 29 June 2017 diff hist 0 N File:DOCK3.7tuturial.2017.06.28.9.png No edit summary current
- 18:2718:27, 29 June 2017 diff hist +1,168 DOCK 3.7 tutorial based on Webinar 2017/06/28 →Scenario 2:
- 18:2418:24, 29 June 2017 diff hist +183 DOCK 3.7 tutorial based on Webinar 2017/06/28 →Scenario 2:
- 18:2218:22, 29 June 2017 diff hist +294 DOCK 3.7 tutorial based on Webinar 2017/06/28 No edit summary
- 18:2218:22, 29 June 2017 diff hist 0 N File:DOCK3.7tuturial.2017.06.28.8.png No edit summary current
- 18:1718:17, 29 June 2017 diff hist 0 N File:DOCK3.7tuturial.2017.06.28.7.png No edit summary current
- 18:1518:15, 29 June 2017 diff hist 0 N File:DOCK3.7tuturial.2017.06.28.6.png No edit summary current
28 June 2017
- 22:2922:29, 28 June 2017 diff hist +151 DOCK 3.7 tutorial based on Webinar 2017/06/28 No edit summary
- 22:2122:21, 28 June 2017 diff hist +1,102 DOCK 3.7 tutorial based on Webinar 2017/06/28 No edit summary
- 22:2022:20, 28 June 2017 diff hist 0 N File:DOCK3.7tuturial.2017.06.28.5.png No edit summary current
- 22:1722:17, 28 June 2017 diff hist 0 N File:DOCK3.7tuturial.2017.06.28.4.png No edit summary current
- 22:1322:13, 28 June 2017 diff hist 0 N File:DOCK3.7tuturial.2017.06.28.3.png No edit summary current
- 22:0422:04, 28 June 2017 diff hist +856 DOCK 3.7 tutorial based on Webinar 2017/06/28 No edit summary
- 21:5721:57, 28 June 2017 diff hist +599 DOCK 3.7 tutorial based on Webinar 2017/06/28 No edit summary
- 20:1620:16, 28 June 2017 diff hist +732 DOCK 3.7 tutorial based on Webinar 2017/06/28 No edit summary
- 20:1420:14, 28 June 2017 diff hist +62 DOCK 3.7 tutorial based on Webinar 2017/06/28 No edit summary
- 20:1320:13, 28 June 2017 diff hist 0 N File:DOCK3.7tuturial.2017.06.28.2.png No edit summary current
- 20:1120:11, 28 June 2017 diff hist +485 DOCK 3.7 tutorial based on Webinar 2017/06/28 No edit summary
- 20:0820:08, 28 June 2017 diff hist −39 DOCK 3.7 tutorial based on Webinar 2017/06/28 No edit summary
- 20:0720:07, 28 June 2017 diff hist 0 File:DOCK3.7tuturial.2017.06.28.png TBalius uploaded a new version of "File:DOCK3.7tuturial.2017.06.28.png" current
- 19:1419:14, 28 June 2017 diff hist +46 DOCK 3.7 tutorial based on Webinar 2017/06/28 No edit summary
- 19:1019:10, 28 June 2017 diff hist +78 DOCK 3.7 tutorial based on Webinar 2017/06/28 No edit summary
- 19:0919:09, 28 June 2017 diff hist +52 DOCK 3.7 →Start here
- 19:0819:08, 28 June 2017 diff hist 0 N File:DOCK3.7tuturial.2017.06.28.png No edit summary
- 19:0019:00, 28 June 2017 diff hist +158 N DOCK 3.7 tutorial based on Webinar 2017/06/28 Created page with " Scenario 1: Use docking to predicted how Erlotinib (an approved drug) binds to the Epidermal Growth Factor Receptor File:DOCK3.7tuturial.2017.06.28.png"
12 June 2017
- 22:2822:28, 12 June 2017 diff hist +5 Dock3.7 No edit summary current
- 22:2722:27, 12 June 2017 diff hist +49 Dock3.7 No edit summary
- 16:1116:11, 12 June 2017 diff hist +1 DOCK 3.7 tutorial (Anat) →Set docking directories
- 16:0916:09, 12 June 2017 diff hist +9 DOCK 3.7 tutorial (Anat) →Set docking directories
- 16:0816:08, 12 June 2017 diff hist +1 DOCK 3.7 tutorial (Anat) →Set docking directories
- 16:0716:07, 12 June 2017 diff hist +108 DOCK 3.7 tutorial (Anat) →ligand prep
22 May 2017
- 23:0423:04, 22 May 2017 diff hist +153 DOCK 3.7 tart No edit summary
3 May 2017
- 16:2616:26, 3 May 2017 diff hist +99 Tutorial on running Molecular Dynamics for GIST grid generation with scripts 2 No edit summary current
26 April 2017
24 April 2017
- 17:3117:31, 24 April 2017 diff hist −8 DOCK 3.7 2015/04/15 abl1 Tutorial No edit summary
- 17:3017:30, 24 April 2017 diff hist −8 DOCK 3.7 with GIST tutorials No edit summary
- 17:3017:30, 24 April 2017 diff hist +59 DOCK 3.7 with GIST tutorials No edit summary
- 17:3017:30, 24 April 2017 diff hist +60 DOCK 3.7 2015/04/15 abl1 Tutorial No edit summary
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