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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
