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- 23:37, 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
- 23:34, 28 March 2020 diff hist +53 DOCK 3.7 →Start here
- 10:10, 24 March 2020 diff hist +126 Useful chimera commands current
- 10:06, 24 March 2020 diff hist +579 Useful chimera commands
- 13:29, 26 August 2019 diff hist 0 Minimize protein-covalent ligand complex with AMBER current
- 19:32, 25 March 2019 diff hist +38 Install DOCK 3.7 →Installing third-party softwares current
- 18:51, 6 February 2019 diff hist +62 Calculate volume of the binding site and molecules current
- 18:50, 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
- 18:49, 6 February 2019 diff hist +42 Other Useful Stuff
- 20:01, 28 January 2019 diff hist +15 How to do parameter scanning
- 18:41, 26 January 2019 diff hist +36 DOCK 3.7 →Prepare Receptor
- 01:29, 24 January 2019 diff hist +87 Calculate volume of the binding site and molecules →Calculating the volume of a binding site.
- 19:55, 3 January 2019 diff hist +3 Minimize protein-covalent ligand complex with AMBER
- 19:47, 3 January 2019 diff hist 0 Minimize protein-covalent ligand complex with AMBER
- 21:32, 17 December 2018 diff hist 0 File:2018 12 coval1.png TBalius uploaded a new version of "File:2018 12 coval1.png" current
- 21:24, 17 December 2018 diff hist 0 File:2018 12 coval1.png TBalius uploaded a new version of "File:2018 12 coval1.png"
- 21:16, 17 December 2018 diff hist 0 File:2018 12 coval1.png TBalius uploaded a new version of "File:2018 12 coval1.png"
- 20:17, 17 December 2018 diff hist 0 N File:2018 12 coval1.png
- 19:23, 17 December 2018 diff hist +270 Minimize protein-covalent ligand complex with AMBER
- 19:14, 17 December 2018 diff hist +1,302 Minimize protein-covalent ligand complex with AMBER
- 19:10, 17 December 2018 diff hist +1,278 Minimize protein-covalent ligand complex with AMBER
- 19:07, 17 December 2018 diff hist +928 Minimize protein-covalent ligand complex with AMBER
- 19:01, 17 December 2018 diff hist +8,601 Minimize protein-covalent ligand complex with AMBER
- 17:58, 17 December 2018 diff hist +76 Minimize protein-covalent ligand complex with AMBER
- 17:55, 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...."
- 17:19, 17 December 2018 diff hist +58 DOCK 3.7 →Prepare Receptor
- 01:34, 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
- 21:50, 6 December 2018 diff hist -4 How to cite →DOCK 6 current
- 21:49, 6 December 2018 diff hist +279 How to cite
- 17:13, 26 September 2018 diff hist +451 DOCK 3.7 2018/06/05 abl1 Tutorial →combining the results
- 15:45, 26 September 2018 diff hist +970 Rescoring with DOCK 3.7 current
- 18:28, 14 September 2018 diff hist -9 Calculate volume of the binding site and molecules
- 18:26, 14 September 2018 diff hist -2 Calculate volume of the binding site and molecules
- 18:26, 14 September 2018 diff hist +130 Calculate volume of the binding site and molecules
- 18:02, 31 July 2018 diff hist -3 Using thin spheres in DOCK3.7 →Tutorial for using Thin Spheres in DOCK 3.7.1rc1
- 17:12, 20 July 2018 diff hist +53 Sample Additional Ring Puckers current
- 16:14, 20 July 2018 diff hist -11 Sample Additional Ring Puckers
- 16:00, 20 July 2018 diff hist -3 Sample Additional Ring Puckers →new script in developmental version (DOCKBASE = ~tbalius/zzz.github/DOCK)
- 15:50, 20 July 2018 diff hist +1,163 Sample Additional Ring Puckers
- 17:57, 21 June 2018 diff hist +211 Sample Additional Ring Puckers
- 17:48, 21 June 2018 diff hist +38 Sample Additional Ring Puckers
- 17:45, 21 June 2018 diff hist +270 Sample Additional Ring Puckers
- 17:19, 21 June 2018 diff hist 0 Sample Additional Ring Puckers
- 17:19, 21 June 2018 diff hist +133 Sample Additional Ring Puckers
- 16:08, 21 June 2018 diff hist +43 DOCK 3.7
- 16:01, 21 June 2018 diff hist +36 Sample Additional Ring Puckers
- 15:53, 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..."
- 15:52, 20 June 2018 diff hist +74 DOCK 3.7
- 00:45, 12 June 2018 diff hist +31 DOCK 3.7 2018/06/05 abl1 Tutorial →run blastermaster.py
- 00:44, 12 June 2018 diff hist +575 DOCK 3.7 2018/06/05 abl1 Tutorial →run blastermaster.py
- 22:57, 7 June 2018 diff hist +182 Whole Library TC to Knowns Calculations
- 22:16, 7 June 2018 diff hist -5 Whole Library TC to Knowns Calculations
- 15:59, 5 June 2018 diff hist -2,629 DOCK 3.7 2018/06/05 abl1 Tutorial →run enrichment calculations
- 15:56, 5 June 2018 diff hist 0 DOCK 3.7 2015/04/15 abl1 Tutorial current
- 15:56, 5 June 2018 diff hist +75 DOCK 3.7 2015/04/15 abl1 Tutorial
- 15:54, 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..."
- 15:53, 5 June 2018 diff hist +51 DOCK 3.7 →Start here
- 17:15, 4 June 2018 diff hist +224 DOCK 3.7 2015/04/15 abl1 Tutorial →Modify matching spheres
- 21:50, 2 May 2018 diff hist +300 DOCK 3.7 2015/04/15 abl1 Tutorial →combine scores and poses
- 22:42, 16 April 2018 diff hist +54 Ssh tunnel (Trent's way) current
- 22:39, 16 April 2018 diff hist +192 Ssh tunnel (Trent's way)
- 22:32, 16 April 2018 diff hist +100 Ssh tunnel (Trent's way)
- 22:31, 16 April 2018 diff hist -21 Ssh tunnel (Trent's way)
- 22:30, 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..."
- 20:54, 16 April 2018 diff hist +45 Minimize protein-ligand complex with AMBER →Step 2. Prepare ligand charges and force field.
- 17:59, 16 April 2018 diff hist +31 Welcome group members →Access from home
- 16:45, 12 April 2018 diff hist +5 Using thin spheres in DOCK3.7 →Tutorial for using Thin Spheres in DOCK 3.7
- 16:43, 12 April 2018 diff hist +2,085 Using thin spheres in DOCK3.7
- 17:53, 11 April 2018 diff hist +200 Using thin spheres in DOCK3.7
- 20:16, 6 April 2018 diff hist -2 Minimize protein-ligand complex with AMBER →Step 2. Prepare ligand charges and force field.
- 20:09, 6 April 2018 diff hist +431 Minimize protein-ligand complex with AMBER →Step 2. Prepare ligand charges and force field.
- 00:47, 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
- 00:47, 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
- 00:47, 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
- 00:40, 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
- 17:19, 2 April 2018 diff hist +65 Minimize protein-ligand complex with AMBER
- 17:18, 2 April 2018 diff hist -6 Minimize protein-ligand complex with AMBER
- 17:17, 2 April 2018 diff hist +81 Minimize protein-ligand complex with AMBER →Step 1. Break up the complex into ligand (small molecule) and receptor.
- 17:08, 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..."
- 16:30, 2 April 2018 diff hist +49 DOCK 3.7 →Prepare Receptor
- 19:24, 14 February 2018 diff hist +193 Enm explorer current
- 16:16, 2 February 2018 diff hist +433 Enm explorer
- 20:17, 31 January 2018 diff hist +50 How to process results from a large-scale docking →Cluster results
- 19:56, 31 January 2018 diff hist +98 Enm explorer
- 01:25, 31 January 2018 diff hist +103 How to process results from a large-scale docking →Combine results
- 01:24, 31 January 2018 diff hist +116 How to process results from a large-scale docking →Cluster results
- 18:50, 29 November 2017 diff hist +351 Rescoring with DOCK 3.7 →how to generate need files
- 18:36, 29 November 2017 diff hist +201 Rescoring with DOCK 3.7 →how to generate need files
- 18:27, 29 November 2017 diff hist +4,212 Rescoring with DOCK 3.7 →how to generate need files
- 22:53, 17 November 2017 diff hist -1 Ligand preparation - 20170424 →3 ways to build ligands: current
- 19:39, 17 November 2017 diff hist +4 Tutorial on running DOCK3.7 with blury-GIST current
- 19:38, 17 November 2017 diff hist +521 Tutorial on running DOCK3.7 with blury-GIST
- 16:43, 16 November 2017 diff hist +2 Tutorial on running DOCK3.7 with blury-GIST
- 01:31, 16 November 2017 diff hist +138 Tutorial on running DOCK3.7 with GIST →Prepare system for docking current
- 01:30, 16 November 2017 diff hist +133 Tutorial on running DOCK3.7 with GIST →Get ligand databases
- 20:09, 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 ..."
- 19:56, 15 November 2017 diff hist +50 DOCK 3.7 with GIST tutorials current
- 00:19, 15 November 2017 diff hist +42 DOCK3.7 INDOCK Minimization Parameter →Information on number_save and number_write parameters current
- 00:18, 15 November 2017 diff hist +57 DOCK3.7 INDOCK Minimization Parameter →Information on number_save and number_write parameters
- 00:06, 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
- 23:49, 14 November 2017 diff hist 0 N File:Miminizer.2017.11.14.png
- 23:48, 14 November 2017 diff hist +138 DOCK3.7 INDOCK Minimization Parameter →Information on number_save and number_write parameters
- 19:28, 14 November 2017 diff hist +977 DOCK3.7 INDOCK Minimization Parameter
- 23:49, 10 November 2017 diff hist +32 INDOCK 3.7 current
- 22:57, 10 November 2017 diff hist +116 DOCK 3.7 →Running Docking
- 00:18, 9 November 2017 diff hist +1 Tutorial on running Molecular Dynamics for GIST grid generation with scripts current
- 20:03, 8 November 2017 diff hist +98 How to process results from a large-scale docking →Check for completion and resubmit failed jobs
- 20:00, 8 November 2017 diff hist +126 How to process results from a large-scale docking →Check for completion and resubmit failed jobs
- 22:28, 18 October 2017 diff hist +186 How to process results from a large-scale docking
- 22:25, 18 October 2017 diff hist +4 How to process results from a large-scale docking
- 22:24, 18 October 2017 diff hist +92 How to process results from a large-scale docking
- 21:30, 18 October 2017 diff hist +81 How to process results from a large-scale docking →Check for completion and resubmit failed jobs
- 21:28, 18 October 2017 diff hist +93 How to process results from a large-scale docking →Check for completion and resubmit failed jobs
- 18:09, 5 October 2017 diff hist 0 Ligand preparation - 20170424 →3 ways to build ligands:
- 18:09, 5 October 2017 diff hist +69 Ligand preparation - 20170424 →3 ways to build ligands:
- 15:31, 3 October 2017 diff hist -1 DOCK 3.7 tutorial based on Webinar 2017/06/28 →Scenario 2: current
- 15:29, 3 October 2017 diff hist -2 DOCK 3.7 tutorial based on Webinar 2017/06/28 →Scenario 2:
- 15:29, 3 October 2017 diff hist +5 DOCK 3.7 tutorial based on Webinar 2017/06/28 →Scenario 2:
- 15:28, 3 October 2017 diff hist +36 DOCK 3.7 tutorial based on Webinar 2017/06/28 →Scenario 2:
- 15:25, 3 October 2017 diff hist +127 DOCK 3.7 tutorial based on Webinar 2017/06/28 →Scenario 2:
- 15:20, 3 October 2017 diff hist +154 DOCK 3.7 tutorial based on Webinar 2017/06/28 →Scenario 2:
- 16:16, 2 October 2017 diff hist -1 Chimera Tutorial (Delta opioid receptor) current
- 18:26, 29 September 2017 diff hist +1 Using thin spheres in DOCK3.7
- 23:16, 13 September 2017 diff hist -1 ECFP4 Best First Clustering
- 17:48, 6 July 2017 diff hist +40 Mailing address for the Shoichet lab current
- 17:42, 6 July 2017 diff hist +18 Mailing address for the Shoichet lab
- 17:41, 6 July 2017 diff hist +87 Mailing address for the Shoichet lab
- 17:36, 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..."
- 16:05, 30 June 2017 diff hist +82 DOCK 3.7 tutorial based on Webinar 2017/06/28
- 18:32, 29 June 2017 diff hist +458 DOCK 3.7 tutorial based on Webinar 2017/06/28 →Scenario 2:
- 18:32, 29 June 2017 diff hist 0 N File:DOCK3.7tuturial.2017.06.28.9.png current
- 18:27, 29 June 2017 diff hist +1,168 DOCK 3.7 tutorial based on Webinar 2017/06/28 →Scenario 2:
- 18:24, 29 June 2017 diff hist +183 DOCK 3.7 tutorial based on Webinar 2017/06/28 →Scenario 2:
- 18:22, 29 June 2017 diff hist +294 DOCK 3.7 tutorial based on Webinar 2017/06/28
- 18:22, 29 June 2017 diff hist 0 N File:DOCK3.7tuturial.2017.06.28.8.png current
- 18:17, 29 June 2017 diff hist 0 N File:DOCK3.7tuturial.2017.06.28.7.png current
- 18:15, 29 June 2017 diff hist 0 N File:DOCK3.7tuturial.2017.06.28.6.png current
- 22:29, 28 June 2017 diff hist +151 DOCK 3.7 tutorial based on Webinar 2017/06/28
- 22:21, 28 June 2017 diff hist +1,102 DOCK 3.7 tutorial based on Webinar 2017/06/28
- 22:20, 28 June 2017 diff hist 0 N File:DOCK3.7tuturial.2017.06.28.5.png current
- 22:17, 28 June 2017 diff hist 0 N File:DOCK3.7tuturial.2017.06.28.4.png current
- 22:13, 28 June 2017 diff hist 0 N File:DOCK3.7tuturial.2017.06.28.3.png current
- 22:04, 28 June 2017 diff hist +856 DOCK 3.7 tutorial based on Webinar 2017/06/28
- 21:57, 28 June 2017 diff hist +599 DOCK 3.7 tutorial based on Webinar 2017/06/28
- 20:16, 28 June 2017 diff hist +732 DOCK 3.7 tutorial based on Webinar 2017/06/28
- 20:14, 28 June 2017 diff hist +62 DOCK 3.7 tutorial based on Webinar 2017/06/28
- 20:13, 28 June 2017 diff hist 0 N File:DOCK3.7tuturial.2017.06.28.2.png current
- 20:11, 28 June 2017 diff hist +485 DOCK 3.7 tutorial based on Webinar 2017/06/28
- 20:08, 28 June 2017 diff hist -39 DOCK 3.7 tutorial based on Webinar 2017/06/28
- 20:07, 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
- 19:14, 28 June 2017 diff hist +46 DOCK 3.7 tutorial based on Webinar 2017/06/28
- 19:10, 28 June 2017 diff hist +78 DOCK 3.7 tutorial based on Webinar 2017/06/28
- 19:09, 28 June 2017 diff hist +52 DOCK 3.7 →Start here
- 19:08, 28 June 2017 diff hist 0 N File:DOCK3.7tuturial.2017.06.28.png
- 19:00, 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"
- 22:28, 12 June 2017 diff hist +5 Dock3.7 current
- 22:27, 12 June 2017 diff hist +49 Dock3.7
- 16:11, 12 June 2017 diff hist +1 DOCK 3.7 tutorial (Anat) →Set docking directories
- 16:09, 12 June 2017 diff hist +9 DOCK 3.7 tutorial (Anat) →Set docking directories
- 16:08, 12 June 2017 diff hist +1 DOCK 3.7 tutorial (Anat) →Set docking directories
- 16:07, 12 June 2017 diff hist +108 DOCK 3.7 tutorial (Anat) →ligand prep
- 23:04, 22 May 2017 diff hist +153 DOCK 3.7 tart
- 16:26, 3 May 2017 diff hist +99 Tutorial on running Molecular Dynamics for GIST grid generation with scripts 2 current
- 22:00, 26 April 2017 diff hist +578 DOCK 3.7 2015/04/15 abl1 Tutorial →Virtual Screening
- 17:31, 24 April 2017 diff hist -8 DOCK 3.7 2015/04/15 abl1 Tutorial
- 17:30, 24 April 2017 diff hist -8 DOCK 3.7 with GIST tutorials
- 17:30, 24 April 2017 diff hist +59 DOCK 3.7 with GIST tutorials
- 17:30, 24 April 2017 diff hist +60 DOCK 3.7 2015/04/15 abl1 Tutorial
- 16:52, 19 April 2017 diff hist 0 Tutorial on running DOCK3.7 with GIST →docking
- 16:51, 19 April 2017 diff hist +350 Tutorial on running DOCK3.7 with GIST →prepare system for docking
- 21:00, 18 April 2017 diff hist +3,860 Tutorial on running DOCK3.7 with GIST →enrichment
- 17:52, 18 April 2017 diff hist +5 DOCK 3.7 2015/04/15 abl1 Tutorial →set up directories and get databases
- 17:48, 18 April 2017 diff hist +16 DOCK 3.7 2015/04/15 abl1 Tutorial →run enrichment calculations
- 17:30, 18 April 2017 diff hist -4 Ligand preparation - 20170424 →3 ways to build ligands:
- 17:29, 18 April 2017 diff hist +6 Ligand preparation - 20170424 →3 ways to build ligands:
- 17:27, 18 April 2017 diff hist -4 Ligand preparation - 20170424 →3 ways to build ligands:
- 17:09, 18 April 2017 diff hist +2,390 Ligand preparation - 20170424
- 15:55, 18 April 2017 diff hist +306 Tutorial on running Molecular Dynamics for GIST grid generation with scripts →Run GIST post processing
- 15:14, 18 April 2017 diff hist +288 Tutorial on running Molecular Dynamics for GIST grid generation with scripts 2
- 23:23, 17 April 2017 diff hist +6,859 Tutorial on running DOCK3.7 with GIST →docking
- 23:18, 17 April 2017 diff hist 0 Tutorial on running DOCK3.7 with GIST
- 21:55, 17 April 2017 diff hist +137 DOCK 3.7 2015/04/15 abl1 Tutorial →run enrichment calculations
- 21:37, 17 April 2017 diff hist +118 DOCK 3.7 2015/04/15 abl1 Tutorial →Visualize the docking spheres
- 20:32, 17 April 2017 diff hist +2,551 Tutorial on running DOCK3.7 with GIST →prepare system for docking (flex)
- 19:17, 17 April 2017 diff hist +3,637 Tutorial on running DOCK3.7 with GIST
- 18:48, 17 April 2017 diff hist +98 Tutorial on running Molecular Dynamics for GIST grid generation with scripts
- 18:46, 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..."
- 18:44, 17 April 2017 diff hist +2 Tutorial on running Molecular Dynamics for GIST grid generation with scripts →Prepare for AMBER
- 18:43, 17 April 2017 diff hist +145 Tutorial on running Molecular Dynamics for GIST grid generation with scripts →Prepare for AMBER
- 18:13, 17 April 2017 diff hist +20,538 Tutorial on running Molecular Dynamics for GIST grid generation with scripts →Run GIST post processing
- 17:47, 17 April 2017 diff hist +17,769 Tutorial on running Molecular Dynamics for GIST grid generation with scripts
- 17:24, 17 April 2017 diff hist +9,391 Tutorial on running Molecular Dynamics for GIST grid generation with scripts →Prepare for AMBER
- 17:08, 17 April 2017 diff hist -27 Tutorial on running Molecular Dynamics for GIST grid generation with scripts →Set up directories
- 16:59, 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..."
- 16:56, 17 April 2017 diff hist +83 DOCK 3.7 with GIST tutorials
- 16:55, 17 April 2017 diff hist +73 Tutorial on running DOCK3.7 with GIST
- 16:54, 17 April 2017 diff hist +72 Tutorial on running Molecular Dynamics for GIST grid generation
- 22:10, 14 April 2017 diff hist +121 DOCK 3.7 2015/04/15 abl1 Tutorial →run be_blasti.py
- 21:42, 14 April 2017 diff hist +136 DOCK 3.7 2015/04/15 abl1 Tutorial
- 15:28, 12 April 2017 diff hist +1 Ligand preparation - 20170424
- 00:14, 28 February 2017 diff hist +64 Tutorial on running Molecular Dynamics for GIST grid generation →Prepare for AMBER
- 00:12, 28 February 2017 diff hist +96 Tutorial on running Molecular Dynamics for GIST grid generation →Prepare for AMBER
- 00:01, 28 February 2017 diff hist +14 Tutorial on running Molecular Dynamics for GIST grid generation
- 16:36, 30 January 2017 diff hist +2 Tutorial on running DOCK3.7 with GIST
- 16:35, 30 January 2017 diff hist -5 Tutorial on running DOCK3.7 with GIST
- 16:35, 30 January 2017 diff hist +357 Tutorial on running DOCK3.7 with GIST
- 16:28, 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..."
- 18:19, 24 January 2017 diff hist -79 Tutorial on running Molecular Dynamics for GIST grid generation →Run convergence analysis
- 18:15, 24 January 2017 diff hist +2,704 Tutorial on running Molecular Dynamics for GIST grid generation →Run convergence analysis
- 17:46, 24 January 2017 diff hist -1 Tutorial on running Molecular Dynamics for GIST grid generation →Run convergence analysis
- 17:46, 24 January 2017 diff hist -154 Tutorial on running Molecular Dynamics for GIST grid generation →Run convergence analysis
- 17:45, 24 January 2017 diff hist +2 Tutorial on running Molecular Dynamics for GIST grid generation →Run convergence analysis
- 17:44, 24 January 2017 diff hist +330 Tutorial on running Molecular Dynamics for GIST grid generation →Run GIST post processing
- 17:13, 24 January 2017 diff hist +146 Tutorial on running Molecular Dynamics for GIST grid generation →Run convergence analysis
- 17:11, 24 January 2017 diff hist +1,193 Tutorial on running Molecular Dynamics for GIST grid generation →Run convergence analysis
- 17:04, 24 January 2017 diff hist +84 Tutorial on running Molecular Dynamics for GIST grid generation →Combining GIST grids
- 17:02, 24 January 2017 diff hist +4 Tutorial on running Molecular Dynamics for GIST grid generation →Combining GIST grids
- 17:02, 24 January 2017 diff hist +1,191 Tutorial on running Molecular Dynamics for GIST grid generation →Combining GIST grids
- 19:57, 23 January 2017 diff hist +20 Tutorial on running Molecular Dynamics for GIST grid generation →Disclaimer
- 17:53, 23 January 2017 diff hist +201 Tutorial on running Molecular Dynamics for GIST grid generation →Combining GIST grids
- 17:33, 23 January 2017 diff hist +1,327 Tutorial on running Molecular Dynamics for GIST grid generation →Run GIST post processing
- 17:30, 23 January 2017 diff hist -1 Tutorial on running Molecular Dynamics for GIST grid generation →Run GIST post processing
- 17:29, 23 January 2017 diff hist +1,718 Tutorial on running Molecular Dynamics for GIST grid generation →Run GIST post processing
- 16:34, 23 January 2017 diff hist +1 Tutorial on running Molecular Dynamics for GIST grid generation
- 16:33, 23 January 2017 diff hist -31 Tutorial on running Molecular Dynamics for GIST grid generation
- 16:31, 23 January 2017 diff hist +1,737 Tutorial on running Molecular Dynamics for GIST grid generation
- 18:36, 22 January 2017 diff hist +10,057 Tutorial on running Molecular Dynamics for GIST grid generation →Run AMBER
- 02:27, 22 January 2017 diff hist +41 Tutorial on running Molecular Dynamics for GIST grid generation →Run AMBER
- 02:20, 22 January 2017 diff hist +1 Tutorial on running Molecular Dynamics for GIST grid generation →Prepare for AMBER
- 02:19, 22 January 2017 diff hist +92 Tutorial on running Molecular Dynamics for GIST grid generation →Prepare for AMBER
- 02:15, 22 January 2017 diff hist -18 Tutorial on running Molecular Dynamics for GIST grid generation →Prepare for AMBER
- 02:12, 22 January 2017 diff hist +708 Tutorial on running Molecular Dynamics for GIST grid generation →Prepare for AMBER
- 01:57, 22 January 2017 diff hist +1,854 Tutorial on running Molecular Dynamics for GIST grid generation →Prepare for AMBER
- 01:34, 22 January 2017 diff hist +60 Tutorial on running Molecular Dynamics for GIST grid generation →Set up environment
- 01:34, 22 January 2017 diff hist +78 Tutorial on running Molecular Dynamics for GIST grid generation →Prepare for AMBER
- 01:29, 22 January 2017 diff hist +77 Tutorial on running Molecular Dynamics for GIST grid generation →Prepare for AMBER
- 01:27, 22 January 2017 diff hist +1,496 Tutorial on running Molecular Dynamics for GIST grid generation
- 17:21, 20 January 2017 diff hist +166 Tutorial on running Molecular Dynamics for GIST grid generation
- 19:40, 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..."
- 18:19, 9 January 2017 diff hist +134 Chimera current
- 18:16, 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..."
- 18:13, 9 January 2017 diff hist +27 Useful chimera commands
- 18:12, 9 January 2017 diff hist -1 Chimera Tutorial (AMPC) current
- 18:15, 7 January 2017 diff hist +8 Chimera Tutorial (AMPC)
- 18:14, 7 January 2017 diff hist +41 Chimera Tutorial (AMPC)
- 18:11, 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..."
- 18:05, 7 January 2017 diff hist +19 Useful chimera commands →Command line
- 18:03, 7 January 2017 diff hist +55 Useful chimera commands
- 22:55, 6 January 2017 diff hist -2 Using thin spheres in DOCK3.7 →Tutorial for using Thin Spheres in DOCK 3.7
- 22:54, 6 January 2017 diff hist +104 Using thin spheres in DOCK3.7 →Tutorial for using Thin Spheres in DOCK 3.7
- 22:49, 6 January 2017 diff hist +229 Using thin spheres in DOCK3.7
- 22:37, 6 January 2017 diff hist +68 Using thin spheres in DOCK3.7 →Tutorial for using Thin Spheres in DOCK 3.7
- 22:24, 6 January 2017 diff hist +87 Using thin spheres in DOCK3.7 →Tutorial for using Thin Spheres in DOCK 3.7
- 22:16, 6 January 2017 diff hist +42 Using thin spheres in DOCK3.7 →Tutorial for using Thin Spheres in DOCK 3.7
- 22:15, 6 January 2017 diff hist +488 Using thin spheres in DOCK3.7
- 23:46, 5 January 2017 diff hist -3 DOCK 3.7 with GIST tutorials
- 23:43, 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..."
- 23:40, 5 January 2017 diff hist +35 DOCK 3.7
- 21:19, 14 December 2016 diff hist 0 Using thin spheres in DOCK3.7
- 00:56, 14 December 2016 diff hist +54 Useful chimera commands
- 00:54, 14 December 2016 diff hist -3 Using thin spheres in DOCK3.7
- 00:53, 14 December 2016 diff hist -4 Using thin spheres in DOCK3.7
- 01:59, 7 December 2016 diff hist +20 Calculate volume of the binding site and molecules
- 01:58, 7 December 2016 diff hist +1,474 Calculate volume of the binding site and molecules
- 22:31, 4 December 2016 diff hist +166 Calculate volume of the binding site and molecules
- 22:26, 4 December 2016 diff hist +681 Calculate volume of the binding site and molecules →Calculating the volume of a binding site.
- 22:17, 4 December 2016 diff hist -1 Calculate volume of the binding site and molecules →how the volume calculation works.
- 22:05, 4 December 2016 diff hist +51 Calculate volume of the binding site and molecules →Calculating the volume of a small molecule.
- 22:02, 4 December 2016 diff hist +66 Calculate volume of the binding site and molecules
- 22:01, 4 December 2016 diff hist +298 Calculate volume of the binding site and molecules
- 21:57, 4 December 2016 diff hist +377 Calculate volume of the binding site and molecules
- 21:50, 4 December 2016 diff hist +8 Calculate volume of the binding site and molecules
- 21:49, 4 December 2016 diff hist +1,542 Calculate volume of the binding site and molecules →Calculating the volume of a small molecule.
- 21:42, 4 December 2016 diff hist 0 Calculate volume of the binding site and molecules
- 21:42, 4 December 2016 diff hist +55 Calculate volume of the binding site and molecules
- 21:39, 4 December 2016 diff hist +18 Calculate volume of the binding site and molecules
- 21:38, 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 ..."
- 21:33, 4 December 2016 diff hist +84 N Other Useful Stuff Created page with " Useful chimera commands calculate volume of the binding site and molecules"
- 21:31, 4 December 2016 diff hist 0 DOCK 3.7
- 21:31, 4 December 2016 diff hist +25 DOCK 3.7
- 16:52, 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...."
- 20:21, 18 November 2016 diff hist -6 ZINC15:examples:public
- 19:05, 3 November 2016 diff hist +225 Using thin spheres in DOCK3.7
- 18:51, 3 November 2016 diff hist +32 Using thin spheres in DOCK3.7
- 18:49, 3 November 2016 diff hist -23 Using thin spheres in DOCK3.7
- 18:41, 3 November 2016 diff hist +77 Using thin spheres in DOCK3.7
- 18:25, 3 November 2016 diff hist +32 Using thin spheres in DOCK3.7
- 18:20, 3 November 2016 diff hist +12 Using thin spheres in DOCK3.7
- 18:17, 3 November 2016 diff hist +547 Using thin spheres in DOCK3.7
- 17:20, 3 November 2016 diff hist +98 Using thin spheres in DOCK3.7
- 16:07, 3 November 2016 diff hist +41 Using thin spheres in DOCK3.7
- 15:46, 3 November 2016 diff hist +303 Using thin spheres in DOCK3.7
- 00:10, 3 November 2016 diff hist +119 Using thin spheres in DOCK3.7
- 23:42, 2 November 2016 diff hist -4 Using thin spheres in DOCK3.7
- 22:21, 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..."
- 22:21, 2 November 2016 diff hist -2 DOCK 3.7 tutorial (Anat) →Using modified(existing) delphi spheres:
- 22:20, 2 November 2016 diff hist +36 DOCK 3.7 tutorial (Anat)
- 18:18, 19 September 2016 diff hist +520 DOCK 3.7 2015/04/15 abl1 Tutorial →Modify matching spheres
- 18:05, 19 September 2016 diff hist -2 DOCK 3.7 tart
- 18:05, 19 September 2016 diff hist +137 DOCK 3.7 tart
- 02:06, 19 September 2016 diff hist +58 DOCK 3.7 2015/04/15 abl1 Tutorial →run enrichment calculations
- 02:04, 19 September 2016 diff hist +1 DOCK 3.7 2015/04/15 abl1 Tutorial →run enrichment calculations
- 01:59, 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
- 01:57, 19 September 2016 diff hist +279 DOCK 3.7 2016/09/16 Tutorial for Enrichment Calculations (Trent & Jiankun)
- 01:53, 19 September 2016 diff hist +846 DOCK 3.7 2015/04/15 abl1 Tutorial →run enrichment calculations
- 01:33, 19 September 2016 diff hist 0 DOCK 3.7 2015/04/15 abl1 Tutorial
- 01:26, 19 September 2016 diff hist -84 DOCK 3.7 2016/09/16 Tutorial for Enrichment Calculations (Trent & Jiankun)
- 16:19, 16 September 2016 diff hist +208 DOCK 3.7 2015/04/15 abl1 Tutorial →run blastermaster.py
- 16:11, 16 September 2016 diff hist +410 DOCK 3.7 2015/04/15 abl1 Tutorial →create AUC plot of ligands and decoys
- 19:23, 14 September 2016 diff hist -6 Copying files current
- 19:16, 14 September 2016 diff hist +223 Copying files
- 17:09, 23 May 2016 diff hist +516 INDOCK 3.7
- 23:46, 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. =..."
- 23:37, 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
- 18:01, 8 April 2016 diff hist +177 Install DOCK 3.7
- 17:23, 7 April 2016 diff hist +116 DOCK 3.7 2015/04/15 abl1 Tutorial →curating and hit-picking
- 17:08, 7 April 2016 diff hist +200 DOCK 3.7 2015/04/15 abl1 Tutorial →submitting the docking calculations
- 17:05, 7 April 2016 diff hist +254 DOCK 3.7 2015/04/15 abl1 Tutorial →combining the results
- 16:25, 7 April 2016 diff hist +40 DOCK 3.7 2015/04/15 abl1 Tutorial →submitting the docking calculations
- 16:24, 7 April 2016 diff hist +867 DOCK 3.7 2015/04/15 abl1 Tutorial →database setup
- 21:26, 6 April 2016 diff hist +249 AMSOL
- 20:04, 6 April 2016 diff hist +41 DOCK 3.7 tutorial (Anat) →ligand prep
- 20:02, 6 April 2016 diff hist -2 DOCK 3.7 tutorial (Anat) →ligand prep
- 15:26, 5 April 2016 diff hist +93 History of DOCK 6 →Version 3.5 current
- 16:51, 26 January 2016 diff hist +42 DOCK 3.7 tutorial (Anat) →Using modified(existing) matching spheres:
- 16:48, 26 January 2016 diff hist +539 DOCK 3.7 tutorial (Anat)
- 19:40, 25 January 2016 diff hist +443 DOCK 3.7 tutorial (Anat)
- 18:01, 12 October 2015 diff hist +7 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 17:56, 12 October 2015 diff hist 0 DOCK 3.7 2015/04/15 abl1 Tutorial
- 17:51, 12 October 2015 diff hist +260 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 22:10, 2 October 2015 diff hist +1 ZINC15:update policy
- 21:26, 11 September 2015 diff hist +73 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 21:09, 11 September 2015 diff hist +2 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 21:09, 11 September 2015 diff hist +84 DOCK 3.7 2015/04/15 abl1 Tutorial
- 21:22, 15 July 2015 diff hist +110 How to compile DOCK →profiling dock
- 17:24, 29 June 2015 diff hist +40 DOCK 3.7 tutorial (Anat)
- 17:21, 29 June 2015 diff hist +101 DOCK 3.7 tutorial (Anat)
- 22:45, 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..."
- 22:35, 25 June 2015 diff hist +31 DOCK 3.7 →Start here
- 16:22, 18 June 2015 diff hist +142 Trent scripts current
- 18:22, 29 May 2015 diff hist +25 Install DOCK 3.7
- 18:20, 29 May 2015 diff hist +102 Amsol 7 patch current
- 15:54, 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"
- 22:36, 12 May 2015 diff hist +1,463 DOCKovalent 3.7 →Sending a run
- 21:17, 12 May 2015 diff hist +42 DOCKovalent 3.7 →INDOCK parameters
- 19:22, 12 May 2015 diff hist -12 DOCKovalent 3.7 →Sending a run
- 18:45, 12 May 2015 diff hist +406 DOCKovalent 3.7 →General setup
- 18:34, 12 May 2015 diff hist +143 DOCKovalent 3.7 →General setup
- 18:31, 12 May 2015 diff hist +167 DOCKovalent 3.7 →General setup
- 23:57, 23 April 2015 diff hist +42 DOCK 3.7 2015/04/15 abl1 Tutorial →make the hing region more polar
- 23:56, 23 April 2015 diff hist +1 DOCK 3.7 tart
- 17:50, 23 April 2015 diff hist 0 DOCK 3.7 2015/04/15 abl1 Tutorial →make the hing regen more polar
- 00:16, 23 April 2015 diff hist +69 DOCK 3.7 2015/04/15 abl1 Tutorial
- 16:59, 19 April 2015 diff hist +11 DOCK 3.7 2015/04/15 abl1 Tutorial
- 14:13, 19 April 2015 diff hist +149 DOCK 3.7 2015/04/15 abl1 Tutorial
- 00:35, 18 April 2015 diff hist +3,934 DOCK 3.7 2015/04/15 abl1 Tutorial →improving docking
- 00:24, 18 April 2015 diff hist 0 N File:Modspheres.png current
- 00:24, 18 April 2015 diff hist +305 DOCK 3.7 2015/04/15 abl1 Tutorial
- 00:17, 18 April 2015 diff hist +73 DOCK 3.7 2015/04/15 abl1 Tutorial →combine scores and poses
- 00:16, 18 April 2015 diff hist 0 N File:Decoydock.png current
- 00:15, 18 April 2015 diff hist 0 N File:Liganddock.png current
- 00:14, 18 April 2015 diff hist -1 DOCK 3.7 2015/04/15 abl1 Tutorial →create AUC plot of ligands and decoys
- 21:06, 17 April 2015 diff hist +7 DOCK 3.7 2015/04/15 abl1 Tutorial →run blastermaster.py
- 21:06, 17 April 2015 diff hist +187 DOCK 3.7 2015/04/15 abl1 Tutorial →combine scores and poses
- 20:47, 17 April 2015 diff hist +414 DOCK 3.7 2015/04/15 abl1 Tutorial →create AUC plot of ligands and decoys
- 20:44, 17 April 2015 diff hist 0 N File:AblROCplot.png current
- 20:44, 17 April 2015 diff hist +166 DOCK 3.7 2015/04/15 abl1 Tutorial →create AUC plot of ligands and decoys
- 20:41, 17 April 2015 diff hist 0 N File:Spheresbox.png current
- 20:40, 17 April 2015 diff hist +255 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 20:36, 17 April 2015 diff hist +22 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 20:36, 17 April 2015 diff hist -2 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 20:34, 17 April 2015 diff hist +94 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 20:31, 17 April 2015 diff hist -2 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 20:27, 17 April 2015 diff hist +3,924 DOCK 3.7 2015/04/15 abl1 Tutorial
- 20:20, 17 April 2015 diff hist +2,575 DOCK 3.7 2015/04/15 abl1 Tutorial
- 20:10, 17 April 2015 diff hist -9 DOCK 3.7 2015/04/15 abl1 Tutorial →run enrichment calucaltions
- 20:09, 17 April 2015 diff hist -98 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 20:07, 17 April 2015 diff hist 0 File:Spheres.png TBalius uploaded a new version of "File:Spheres.png" current
- 20:06, 17 April 2015 diff hist 0 N File:Spheres.png
- 20:04, 17 April 2015 diff hist +9 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 20:03, 17 April 2015 diff hist -16 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 20:03, 17 April 2015 diff hist +105 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 20:02, 17 April 2015 diff hist +38 DOCK 3.7 2015/04/15 abl1 Tutorial →visualize the docking spheres
- 20:00, 17 April 2015 diff hist +156 DOCK 3.7 2015/04/15 abl1 Tutorial →run blastermaster.py
- 22:40, 15 April 2015 diff hist -12 DOCK 3.7 2015/04/15 abl1 Tutorial
- 22:17, 15 April 2015 diff hist +6 DOCK 3.7 2015/04/15 abl1 Tutorial
- 22:02, 15 April 2015 diff hist +275 DOCK 3.7 2015/04/15 abl1 Tutorial →run blastermaster.py
- 21:46, 15 April 2015 diff hist -3,782 DOCK 3.7 2015/04/15 abl1 Tutorial
- 21:43, 15 April 2015 diff hist +5,528 DOCK 3.7 2015/04/15 abl1 Tutorial
- 21:41, 15 April 2015 diff hist +3,686 DOCK 3.7 2015/04/15 abl1 Tutorial →run blastermaster.py
- 21:35, 15 April 2015 diff hist 0 N File:Rec lig 2HYY.png current
- 21:32, 15 April 2015 diff hist +420 DOCK 3.7 2015/04/15 abl1 Tutorial →run be_blasti.py
- 21:25, 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..." current
- 21:21, 15 April 2015 diff hist +2,479 DOCK 3.7 2015/04/15 abl1 Tutorial →run be_blasti.py
- 21:11, 15 April 2015 diff hist -37 DOCK 3.7 2015/04/15 abl1 Tutorial
- 21:10, 15 April 2015 diff hist +101 DOCK 3.7 2015/04/15 abl1 Tutorial
- 21:09, 15 April 2015 diff hist +116 DOCK 3.7 2015/04/15 abl1 Tutorial →set up directories and get databases
- 21:05, 15 April 2015 diff hist +18 DOCK 3.7 2015/04/15 abl1 Tutorial
- 21:04, 15 April 2015 diff hist +1,212 DOCK 3.7 2015/04/15 abl1 Tutorial →set up a directory
- 20:40, 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..."
- 20:36, 15 April 2015 diff hist +40 DOCK 3.7
- 22:49, 19 March 2015 diff hist +86 Physical property space →Property Space
- 17:09, 6 March 2015 diff hist +223 How to compile DOCK
- 19:53, 5 March 2015 diff hist -5 How to compile DOCK →debuging dock
- 19:52, 5 March 2015 diff hist +663 How to compile DOCK
- 19:36, 5 March 2015 diff hist +1 Install DOCK 3.7
- 15:46, 23 October 2014 diff hist +87 Mol2db2 current
- 15:45, 23 October 2014 diff hist +58 DOCK 3.7
- 15:44, 23 October 2014 diff hist +293 Mol2db2 Format 2 current
- 17:45, 26 September 2014 diff hist +65 DOCK 3.7 2014/09/25 FXa Tutorial
- 17:41, 26 September 2014 diff hist +52 N File:Veiwdock.FXa.frag.top200.png chimera veiwdock session for FXa with top 200 frags. current
- 17:38, 26 September 2014 diff hist +64 DOCK 3.7 2014/09/25 FXa Tutorial →pose visualization
- 13:06, 26 September 2014 diff hist +15 DOCK 3.7 2014/09/25 FXa Tutorial →Receptor Preparation
- 13:05, 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
- 13:05, 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
- 12:56, 26 September 2014 diff hist +62 DOCK 3.7 2014/09/25 FXa Tutorial
- 12:55, 26 September 2014 diff hist +377 DOCK 3.7 2014/09/25 FXa Tutorial
- 12:49, 26 September 2014 diff hist +348 DOCK 3.7 2014/09/25 FXa Tutorial →Receptor Preparation
- 12:43, 26 September 2014 diff hist +2,005 DOCK 3.7 2014/09/25 FXa Tutorial →Receptor Preparation
- 12:35, 26 September 2014 diff hist +18 DOCK 3.7 2014/09/25 FXa Tutorial →Receptor Preparation
- 12:32, 26 September 2014 diff hist -1 DOCK 3.7 2014/09/25 FXa Tutorial →Receptor Preparation
- 12:31, 26 September 2014 diff hist -55 DOCK 3.7 2014/09/25 FXa Tutorial →Receptor Preparation
- 12:29, 26 September 2014 diff hist +12 DOCK 3.7 2014/09/25 FXa Tutorial →This part of the tutorial uses the release version of DOCK3.7-beta.1.0.1.
- 12:27, 26 September 2014 diff hist +5 DOCK 3.7 2014/09/25 FXa Tutorial →Receptor Preparation
- 12:26, 26 September 2014 diff hist -3 DOCK 3.7 2014/09/25 FXa Tutorial →Receptor Preparation
- 12:25, 26 September 2014 diff hist +2,405 DOCK 3.7 2014/09/25 FXa Tutorial →Receptor Preparation
- 12:09, 26 September 2014 diff hist +292 DOCK 3.7 2014/09/25 FXa Tutorial
- 12:06, 26 September 2014 diff hist +1,111 DOCK 3.7 2014/09/25 FXa Tutorial →This part of the tutorial uses the release version of DOCK3.7-beta.1.0.1.
- 11:51, 26 September 2014 diff hist +7 DOCK 3.7 2014/09/25 FXa Tutorial →Receptor Preparation
- 11:51, 26 September 2014 diff hist +739 DOCK 3.7 2014/09/25 FXa Tutorial →Receptor Preparation
- 00:31, 26 September 2014 diff hist +41 DOCK 3.7 2014/09/25 FXa Tutorial →This part of the tutorial uses the release version of DOCK3.7-beta.1.0.1.
- 23:32, 25 September 2014 diff hist +2 DOCK 3.7 2014/09/25 FXa Tutorial
- 23:29, 25 September 2014 diff hist +218 DOCK 3.7 2014/09/25 FXa Tutorial
- 23:23, 25 September 2014 diff hist +45 N File:Lowdiele.png This the low dielectric sphere for Factor Xa. current
- 23:22, 25 September 2014 diff hist +21 N File:Match.png FXa matching spheres. current
- 23:21, 25 September 2014 diff hist +36 N File:Sphgenall.png FXa with sphgen all sphere clusters. current
- 23:20, 25 September 2014 diff hist +127 DOCK 3.7 2014/09/25 FXa Tutorial →Receptor Preparation
- 22:07, 25 September 2014 diff hist +107 DOCK 3.7 2014/09/25 FXa Tutorial →This part of the tutorial uses the GIST development version of DOCK
- 21:59, 25 September 2014 diff hist -3 DOCK 3.7 2014/09/25 FXa Tutorial →Receptor Preparation
- 21:58, 25 September 2014 diff hist +98 DOCK 3.7 2014/09/25 FXa Tutorial
- 21:26, 25 September 2014 diff hist +10 Installing msms
- 21:25, 25 September 2014 diff hist -9 Installing msms
- 21:24, 25 September 2014 diff hist +493 N Installing msms Created page with "## installation notes. Make a directory: mkdir msms go to the dir: cd /your/path/msms Get it from the web: wget http://mgltools.scripps.edu/downloads/tars/releases/MSMSREL..."
- 21:16, 25 September 2014 diff hist +64 Install DOCK 3.7
- 20:54, 25 September 2014 diff hist +143 DOCK 3.7 2014/09/25 FXa Tutorial →This part of the tutorial uses the release version of DOCK3.7-beta.1.0.1.
- 19:20, 25 September 2014 diff hist +2 DOCK 3.7 2014/09/25 FXa Tutorial →This part of the tutorial uses the release version of DOCK3.7-beta.1.0.1.
- 19:20, 25 September 2014 diff hist +356 DOCK 3.7 2014/09/25 FXa Tutorial
- 18:47, 25 September 2014 diff hist +19 DOCK 3.7 2014/09/25 FXa Tutorial
- 18:47, 25 September 2014 diff hist +19 DOCK 3.7 2014/09/25 FXa Tutorial
- 18:35, 25 September 2014 diff hist +874 N DOCK 3.7 2014/09/25 FXa Tutorial Created page with " Written by Trent E Balius and Crystal Nguyen on 2014/09/25 == This part of the tutorial uses the release version of DOCK3.7-beta.1.0.1. == see the following for requirement..."
- 17:18, 25 September 2014 diff hist +39 DOCK 3.7
- 22:29, 21 September 2014 diff hist +237 Install DOCK 3.7
- 22:57, 13 September 2014 diff hist +161 Install DOCK 3.7
- 22:48, 13 September 2014 diff hist +110 Install DOCK 3.7
- 22:44, 13 September 2014 diff hist +61 Install DOCK 3.7
- 22:41, 13 September 2014 diff hist +218 Install DOCK 3.7
- 18:50, 27 August 2014 diff hist +9 Github →Fork for Development current
- 18:34, 27 August 2014 diff hist +102 Github
- 18:20, 27 August 2014 diff hist +206 Github →Set up for ssh access
- 18:53, 24 July 2014 diff hist -4 Github
- 23:38, 22 July 2014 diff hist 0 DOCK on cygwin current
- 23:37, 22 July 2014 diff hist 0 DOCK on cygwin
- 23:37, 22 July 2014 diff hist -1 DOCK on cygwin
- 23:34, 22 July 2014 diff hist -1 DOCK on cygwin
- 23:33, 22 July 2014 diff hist +62 DOCK on cygwin
- 23:32, 22 July 2014 diff hist +207 DOCK on cygwin
- 21:08, 6 June 2014 diff hist +159 Copying files
- 20:54, 6 June 2014 diff hist +28 Disk types
- 20:45, 6 June 2014 diff hist +2 Automated Database Preparation →Automatic Decoy Generation current
- 20:45, 6 June 2014 diff hist +183 Automated Database Preparation →Automatic Decoy Generation
- 12:42, 14 March 2014 diff hist 0 BKS lab Structure preparation →Preparing cofactors or nonstandard residue for receptor current
- 12:41, 14 March 2014 diff hist -6 BKS lab Structure preparation
- 16:39, 8 November 2013 diff hist +657 Automated Database Preparation →Automatic Decoy Generation
- 14:24, 28 October 2013 diff hist +24 Checkout dockenv →How to check out SEA
- 20:49, 8 October 2013 diff hist +154 DOCK 3.7
- 20:45, 8 October 2013 diff hist +14 DOCK 3
- 20:45, 8 October 2013 diff hist +53 DOCK 3 →History
- 14:49, 9 September 2013 diff hist +2 DOCK Overview →(A) Sphere Centers
- 14:46, 9 September 2013 diff hist +21 DOCK Overview
- 21:36, 5 September 2013 diff hist +4 Disk types
- 21:32, 5 September 2013 diff hist -40 Disk types
- 21:31, 5 September 2013 diff hist +19 Disk types →scratch
- 21:23, 5 September 2013 diff hist +1 Disk types →scratch
- 21:22, 5 September 2013 diff hist +681 Disk types
- 15:31, 6 August 2013 diff hist +39 Cluster 4
- 15:29, 6 August 2013 diff hist +696 Cluster 4
- 15:17, 6 August 2013 diff hist 0 Cluster 4
- 15:16, 6 August 2013 diff hist +663 Cluster 4
- 14:58, 6 August 2013 diff hist +2 Cluster 4
- 14:58, 6 August 2013 diff hist +171 N Cluster 4 Created page with "This instructions are intended for Shoichet lab members. (1) Register with the Compute Canada Database (CCDB): (1.1) go to the following page and click Register (1.2)"
- 14:33, 6 August 2013 diff hist +2 About our cluster
- 14:33, 6 August 2013 diff hist +67 About our cluster
- 16:05, 24 July 2013 diff hist +19 Disk types
- 15:04, 24 July 2013 diff hist +80 Using local Subversion Repository (SVN)
- 22:34, 23 January 2013 diff hist +3 BKS lab Structure preparation
- 22:34, 23 January 2013 diff hist +123 BKS lab Structure preparation
- 19:24, 22 January 2013 diff hist -2 BKS lab Structure preparation →Preparing cofactors or nonstandard residue for receptor
- 19:21, 22 January 2013 diff hist +207 BKS lab Structure preparation
- 23:13, 2 January 2013 diff hist +3 BKS lab Structure preparation →Preparing cofactors or nonstandard residue for receptor
- 23:11, 2 January 2013 diff hist +15 BKS lab Structure preparation →Preparing cofactors or nonstandard residue for receptor
