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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
