User contributions for TBalius

17 December 2018

• 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

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: