User contributions for TBalius
Jump to navigation
Jump to search
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
6 January 2017
- 22:5522:55, 6 January 2017 diff hist −2 Using thin spheres in DOCK3.7 →Tutorial for using Thin Spheres in DOCK 3.7
- 22:5422:54, 6 January 2017 diff hist +104 Using thin spheres in DOCK3.7 →Tutorial for using Thin Spheres in DOCK 3.7
- 22:4922:49, 6 January 2017 diff hist +229 Using thin spheres in DOCK3.7 No edit summary
- 22:3722:37, 6 January 2017 diff hist +68 Using thin spheres in DOCK3.7 →Tutorial for using Thin Spheres in DOCK 3.7
- 22:2422:24, 6 January 2017 diff hist +87 Using thin spheres in DOCK3.7 →Tutorial for using Thin Spheres in DOCK 3.7
- 22:1622:16, 6 January 2017 diff hist +42 Using thin spheres in DOCK3.7 →Tutorial for using Thin Spheres in DOCK 3.7
- 22:1522:15, 6 January 2017 diff hist +488 Using thin spheres in DOCK3.7 No edit summary
5 January 2017
- 23:4623:46, 5 January 2017 diff hist −3 DOCK 3.7 with GIST tutorials No edit summary
- 23:4323:43, 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..."
- 23:4023:40, 5 January 2017 diff hist +35 DOCK 3.7 No edit summary
14 December 2016
- 21:1921:19, 14 December 2016 diff hist 0 Using thin spheres in DOCK3.7 No edit summary
- 00:5600:56, 14 December 2016 diff hist +54 Useful chimera commands No edit summary
- 00:5400:54, 14 December 2016 diff hist −3 Using thin spheres in DOCK3.7 No edit summary
- 00:5300:53, 14 December 2016 diff hist −4 Using thin spheres in DOCK3.7 No edit summary
7 December 2016
- 01:5901:59, 7 December 2016 diff hist +20 Calculate volume of the binding site and molecules No edit summary
- 01:5801:58, 7 December 2016 diff hist +1,474 Calculate volume of the binding site and molecules No edit summary
4 December 2016
- 22:3122:31, 4 December 2016 diff hist +166 Calculate volume of the binding site and molecules No edit summary
- 22:2622:26, 4 December 2016 diff hist +681 Calculate volume of the binding site and molecules →Calculating the volume of a binding site.
- 22:1722:17, 4 December 2016 diff hist −1 Calculate volume of the binding site and molecules →how the volume calculation works.
- 22:0522:05, 4 December 2016 diff hist +51 Calculate volume of the binding site and molecules →Calculating the volume of a small molecule.
- 22:0222:02, 4 December 2016 diff hist +66 Calculate volume of the binding site and molecules No edit summary
- 22:0122:01, 4 December 2016 diff hist +298 Calculate volume of the binding site and molecules No edit summary
- 21:5721:57, 4 December 2016 diff hist +377 Calculate volume of the binding site and molecules No edit summary
- 21:5021:50, 4 December 2016 diff hist +8 Calculate volume of the binding site and molecules No edit summary
- 21:4921:49, 4 December 2016 diff hist +1,542 Calculate volume of the binding site and molecules →Calculating the volume of a small molecule.
- 21:4221:42, 4 December 2016 diff hist 0 Calculate volume of the binding site and molecules No edit summary
- 21:4221:42, 4 December 2016 diff hist +55 Calculate volume of the binding site and molecules No edit summary
- 21:3921:39, 4 December 2016 diff hist +18 Calculate volume of the binding site and molecules No edit summary
- 21:3821:38, 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 ..."
- 21:3321:33, 4 December 2016 diff hist +84 N Other Useful Stuff Created page with " Useful chimera commands calculate volume of the binding site and molecules"
- 21:3121:31, 4 December 2016 diff hist 0 DOCK 3.7 No edit summary
- 21:3121:31, 4 December 2016 diff hist +25 DOCK 3.7 No edit summary
2 December 2016
- 16:5216:52, 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...."
18 November 2016
- 20:2120:21, 18 November 2016 diff hist −6 ZINC15:examples:public No edit summary
3 November 2016
- 19:0519:05, 3 November 2016 diff hist +225 Using thin spheres in DOCK3.7 No edit summary
- 18:5118:51, 3 November 2016 diff hist +32 Using thin spheres in DOCK3.7 No edit summary
- 18:4918:49, 3 November 2016 diff hist −23 Using thin spheres in DOCK3.7 No edit summary
- 18:4118:41, 3 November 2016 diff hist +77 Using thin spheres in DOCK3.7 No edit summary
- 18:2518:25, 3 November 2016 diff hist +32 Using thin spheres in DOCK3.7 No edit summary
- 18:2018:20, 3 November 2016 diff hist +12 Using thin spheres in DOCK3.7 No edit summary
- 18:1718:17, 3 November 2016 diff hist +547 Using thin spheres in DOCK3.7 No edit summary
- 17:2017:20, 3 November 2016 diff hist +98 Using thin spheres in DOCK3.7 No edit summary
- 16:0716:07, 3 November 2016 diff hist +41 Using thin spheres in DOCK3.7 No edit summary
- 15:4615:46, 3 November 2016 diff hist +303 Using thin spheres in DOCK3.7 No edit summary
- 00:1000:10, 3 November 2016 diff hist +119 Using thin spheres in DOCK3.7 No edit summary
2 November 2016
- 23:4223:42, 2 November 2016 diff hist −4 Using thin spheres in DOCK3.7 No edit summary
- 22:2122:21, 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..."
- 22:2122:21, 2 November 2016 diff hist −2 DOCK 3.7 tutorial (Anat) →Using modified(existing) delphi spheres:
- 22:2022:20, 2 November 2016 diff hist +36 DOCK 3.7 tutorial (Anat) No edit summary
19 September 2016
- 18:1818:18, 19 September 2016 diff hist +520 DOCK 3.7 2015/04/15 abl1 Tutorial →Modify matching spheres
- 18:0518:05, 19 September 2016 diff hist −2 DOCK 3.7 tart No edit summary
- 18:0518:05, 19 September 2016 diff hist +137 DOCK 3.7 tart No edit summary
- 02:0602:06, 19 September 2016 diff hist +58 DOCK 3.7 2015/04/15 abl1 Tutorial →run enrichment calculations
- 02:0402:04, 19 September 2016 diff hist +1 DOCK 3.7 2015/04/15 abl1 Tutorial →run enrichment calculations
- 01:5901:59, 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
- 01:5701:57, 19 September 2016 diff hist +279 DOCK 3.7 2016/09/16 Tutorial for Enrichment Calculations (Trent & Jiankun) No edit summary
- 01:5301:53, 19 September 2016 diff hist +846 DOCK 3.7 2015/04/15 abl1 Tutorial →run enrichment calculations
- 01:3301:33, 19 September 2016 diff hist 0 DOCK 3.7 2015/04/15 abl1 Tutorial No edit summary
- 01:2601:26, 19 September 2016 diff hist −84 DOCK 3.7 2016/09/16 Tutorial for Enrichment Calculations (Trent & Jiankun) No edit summary
16 September 2016
- 16:1916:19, 16 September 2016 diff hist +208 DOCK 3.7 2015/04/15 abl1 Tutorial →run blastermaster.py
- 16:1116:11, 16 September 2016 diff hist +410 DOCK 3.7 2015/04/15 abl1 Tutorial →create AUC plot of ligands and decoys
14 September 2016
- 19:2319:23, 14 September 2016 diff hist −6 Copying files No edit summary current
- 19:1619:16, 14 September 2016 diff hist +223 Copying files No edit summary
23 May 2016
- 17:0917:09, 23 May 2016 diff hist +516 INDOCK 3.7 No edit summary
26 April 2016
- 23:4623:46, 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. =..."
- 23:3723:37, 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
8 April 2016
- 18:0118:01, 8 April 2016 diff hist +177 Install DOCK 3.7 No edit summary
7 April 2016
- 17:2317:23, 7 April 2016 diff hist +116 DOCK 3.7 2015/04/15 abl1 Tutorial →curating and hit-picking
- 17:0817:08, 7 April 2016 diff hist +200 DOCK 3.7 2015/04/15 abl1 Tutorial →submitting the docking calculations
- 17:0517:05, 7 April 2016 diff hist +254 DOCK 3.7 2015/04/15 abl1 Tutorial →combining the results