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
- 19:3219:32, 25 March 2019 diff hist +38 Install DOCK 3.7 →Installing third-party softwares current
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