User contributions
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- 16:37, 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)
- 16:34, 28 March 2020 (diff | hist) . . (+53) . . DOCK 3.7 (→Start here)
- 03:10, 24 March 2020 (diff | hist) . . (+126) . . Useful chimera commands (current)
- 03:06, 24 March 2020 (diff | hist) . . (+579) . . Useful chimera commands
- 06:29, 26 August 2019 (diff | hist) . . (0) . . Minimize protein-covalent ligand complex with AMBER (current)
- 12:32, 25 March 2019 (diff | hist) . . (+38) . . Install DOCK 3.7 (→Installing third-party softwares) (current)
- 11:51, 6 February 2019 (diff | hist) . . (+62) . . Calculate volume of the binding site and molecules (current)
- 11:50, 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)
- 11:49, 6 February 2019 (diff | hist) . . (+42) . . Other Useful Stuff
- 13:01, 28 January 2019 (diff | hist) . . (+15) . . How to do parameter scanning
- 11:41, 26 January 2019 (diff | hist) . . (+36) . . DOCK 3.7 (→Prepare Receptor)
- 18:29, 23 January 2019 (diff | hist) . . (+87) . . Calculate volume of the binding site and molecules (→Calculating the volume of a binding site.)
- 12:55, 3 January 2019 (diff | hist) . . (+3) . . Minimize protein-covalent ligand complex with AMBER
- 12:47, 3 January 2019 (diff | hist) . . (0) . . Minimize protein-covalent ligand complex with AMBER
- 14:32, 17 December 2018 (diff | hist) . . (0) . . File:2018 12 coval1.png (TBalius uploaded a new version of "File:2018 12 coval1.png") (current)
- 14:24, 17 December 2018 (diff | hist) . . (0) . . File:2018 12 coval1.png (TBalius uploaded a new version of "File:2018 12 coval1.png")
- 14:16, 17 December 2018 (diff | hist) . . (0) . . File:2018 12 coval1.png (TBalius uploaded a new version of "File:2018 12 coval1.png")
- 13:17, 17 December 2018 (diff | hist) . . (0) . . N File:2018 12 coval1.png
- 12:23, 17 December 2018 (diff | hist) . . (+270) . . Minimize protein-covalent ligand complex with AMBER
- 12:14, 17 December 2018 (diff | hist) . . (+1,302) . . Minimize protein-covalent ligand complex with AMBER
- 12:10, 17 December 2018 (diff | hist) . . (+1,278) . . Minimize protein-covalent ligand complex with AMBER
- 12:07, 17 December 2018 (diff | hist) . . (+928) . . Minimize protein-covalent ligand complex with AMBER
- 12:01, 17 December 2018 (diff | hist) . . (+8,601) . . Minimize protein-covalent ligand complex with AMBER
- 10:58, 17 December 2018 (diff | hist) . . (+76) . . Minimize protein-covalent ligand complex with AMBER
- 10:55, 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....")
- 10:19, 17 December 2018 (diff | hist) . . (+58) . . DOCK 3.7 (→Prepare Receptor)
- 18:34, 14 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)
- 14:50, 6 December 2018 (diff | hist) . . (-4) . . How to cite (→DOCK 6) (current)
- 14:49, 6 December 2018 (diff | hist) . . (+279) . . How to cite
- 10:13, 26 September 2018 (diff | hist) . . (+451) . . DOCK 3.7 2018/06/05 abl1 Tutorial (→combining the results)
- 08:45, 26 September 2018 (diff | hist) . . (+970) . . Rescoring with DOCK 3.7 (current)
- 11:28, 14 September 2018 (diff | hist) . . (-9) . . Calculate volume of the binding site and molecules
- 11:26, 14 September 2018 (diff | hist) . . (-2) . . Calculate volume of the binding site and molecules
- 11:26, 14 September 2018 (diff | hist) . . (+130) . . Calculate volume of the binding site and molecules
- 11:02, 31 July 2018 (diff | hist) . . (-3) . . Using thin spheres in DOCK3.7 (→Tutorial for using Thin Spheres in DOCK 3.7.1rc1)
- 10:12, 20 July 2018 (diff | hist) . . (+53) . . Sample Additional Ring Puckers (current)
- 09:14, 20 July 2018 (diff | hist) . . (-11) . . Sample Additional Ring Puckers
- 09:00, 20 July 2018 (diff | hist) . . (-3) . . Sample Additional Ring Puckers (→new script in developmental version (DOCKBASE = ~tbalius/zzz.github/DOCK))
- 08:50, 20 July 2018 (diff | hist) . . (+1,163) . . Sample Additional Ring Puckers
- 10:57, 21 June 2018 (diff | hist) . . (+211) . . Sample Additional Ring Puckers
- 10:48, 21 June 2018 (diff | hist) . . (+38) . . Sample Additional Ring Puckers
- 10:45, 21 June 2018 (diff | hist) . . (+270) . . Sample Additional Ring Puckers
- 10:19, 21 June 2018 (diff | hist) . . (0) . . Sample Additional Ring Puckers
- 10:19, 21 June 2018 (diff | hist) . . (+133) . . Sample Additional Ring Puckers
- 09:08, 21 June 2018 (diff | hist) . . (+43) . . DOCK 3.7
- 09:01, 21 June 2018 (diff | hist) . . (+36) . . Sample Additional Ring Puckers
- 08:53, 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...")
- 08:52, 20 June 2018 (diff | hist) . . (+74) . . DOCK 3.7
- 17:45, 11 June 2018 (diff | hist) . . (+31) . . DOCK 3.7 2018/06/05 abl1 Tutorial (→run blastermaster.py)
- 17:44, 11 June 2018 (diff | hist) . . (+575) . . DOCK 3.7 2018/06/05 abl1 Tutorial (→run blastermaster.py)
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