User contributions for Rstein
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15 May 2020
- 18:0718:07, 15 May 2020 diff hist −29 Matching Sphere Scan No edit summary
- 18:0518:05, 15 May 2020 diff hist +14 Matching Sphere Scan No edit summary
- 18:0418:04, 15 May 2020 diff hist +12 Matching Sphere Scan No edit summary
- 18:0318:03, 15 May 2020 diff hist −1 Matching Sphere Scan No edit summary
- 18:0318:03, 15 May 2020 diff hist +242 Matching Sphere Scan No edit summary
- 18:0018:00, 15 May 2020 diff hist +41 Matching Sphere Scan No edit summary
- 17:5817:58, 15 May 2020 diff hist +52 Matching Sphere Scan No edit summary
- 17:5717:57, 15 May 2020 diff hist −1 Matching Sphere Scan No edit summary
- 17:5717:57, 15 May 2020 diff hist +511 Matching Sphere Scan No edit summary
- 17:4817:48, 15 May 2020 diff hist +99 Matching Sphere Scan No edit summary
- 17:4717:47, 15 May 2020 diff hist −1 Matching Sphere Scan No edit summary
- 17:4717:47, 15 May 2020 diff hist +657 N Matching Sphere Scan Created page with "This script generates some number of directories with perturbed matching spheres. The original script was written by Trent Balius. Wrapper script is written by Reed Stein. Us..."
- 17:4417:44, 15 May 2020 diff hist +26 DOCK 3.7 →Prepare Receptor
24 March 2020
- 21:1521:15, 24 March 2020 diff hist +265 Generating decoys (Reed's way) →Querying ZINC for SMILES
- 21:1221:12, 24 March 2020 diff hist +122 Generating decoys (Reed's way) →Querying ZINC for Protomers
11 March 2020
- 02:0302:03, 11 March 2020 diff hist +18 Generating decoys (Reed's way) No edit summary
- 01:5901:59, 11 March 2020 diff hist −3 Generating decoys (Reed's way) →Querying ZINC for SMILES
- 01:5101:51, 11 March 2020 diff hist +13 Generating decoys (Reed's way) →Step 1) Setting up SMILES directory
- 01:5101:51, 11 March 2020 diff hist +13 Generating decoys (Reed's way) →Step 1) Setting up directories for Protomers
- 01:5001:50, 11 March 2020 diff hist −9 Generating decoys (Reed's way) →Step 3) Assigning accepted protomer decoys to each ligand protomer
- 01:4901:49, 11 March 2020 diff hist −9 Generating decoys (Reed's way) →Step 3) Assigning decoys to ligands
6 March 2020
- 23:2823:28, 6 March 2020 diff hist +29 Generating decoys (Reed's way) →Step 1) Setting up SMILES directory
- 23:2823:28, 6 March 2020 diff hist +29 Generating decoys (Reed's way) →Step 1) Setting up directories for Protomers
30 October 2019
- 19:3919:39, 30 October 2019 diff hist 0 Converting SMILES to Kekule Format No edit summary current
17 October 2019
- 21:1121:11, 17 October 2019 diff hist +237 Converting SMILES to Kekule Format No edit summary
- 21:0421:04, 17 October 2019 diff hist −8 Converting SMILES to Kekule Format No edit summary
- 21:0421:04, 17 October 2019 diff hist +329 N Converting SMILES to Kekule Format Created page with "For adding molecular structures to slides/papers, SMILEs can be converted into Kekule format with the following command: /nfs/soft/jchem/current/bin/molconvert s..."
- 21:0221:02, 17 October 2019 diff hist +41 DOCK 3.7 →Analysis
11 October 2019
- 00:5700:57, 11 October 2019 diff hist −3 Generating decoys (Reed's way) →Querying ZINC for SMILES
- 00:5600:56, 11 October 2019 diff hist −3 Generating decoys (Reed's way) →Step 1) Setting up directories for Protomers
10 October 2019
- 18:5918:59, 10 October 2019 diff hist +535 Protein Target Preparation Updated →Running Blastermaster current
4 October 2019
- 02:1002:10, 4 October 2019 diff hist +25 Protein Target Preparation Updated →Running Blastermaster
3 October 2019
- 17:3117:31, 3 October 2019 diff hist +105 Protein Target Preparation Updated →Useful References
- 17:2817:28, 3 October 2019 diff hist +11 Protein Target Preparation Updated →Running Blastermaster
- 17:2817:28, 3 October 2019 diff hist +144 Protein Target Preparation Updated →Running Blastermaster
- 17:2617:26, 3 October 2019 diff hist +14 Protein Target Preparation Updated →Running Blastermaster
- 17:2417:24, 3 October 2019 diff hist +6 Protein Target Preparation Updated →Useful References
- 17:2417:24, 3 October 2019 diff hist +1,606 Protein Target Preparation Updated No edit summary
- 17:0917:09, 3 October 2019 diff hist −3 Protein Target Preparation Updated →Running Blastermaster
- 17:0817:08, 3 October 2019 diff hist +274 Protein Target Preparation Updated →Running Blastermaster
- 17:0017:00, 3 October 2019 diff hist +596 Protein Target Preparation Updated →Running Blastermaster
28 August 2019
- 21:3821:38, 28 August 2019 diff hist +1,692 Protein Target Preparation Updated →How Blastermaster works
- 21:3021:30, 28 August 2019 diff hist +74 Protein Target Preparation Updated →How Blastermaster works
- 21:2921:29, 28 August 2019 diff hist +251 Protein Target Preparation Updated →How Blastermaster works
- 19:2119:21, 28 August 2019 diff hist 0 Protein Target Preparation Updated →How Blastermaster works
- 19:2019:20, 28 August 2019 diff hist +67 Protein Target Preparation Updated →How Blastermaster works
- 19:1819:18, 28 August 2019 diff hist +21 Protein Target Preparation Updated →How Blastermaster works
- 19:1819:18, 28 August 2019 diff hist +50 Protein Target Preparation Updated →How Blastermaster works
- 19:1719:17, 28 August 2019 diff hist +373 Protein Target Preparation Updated →How Blastermaster works
- 18:0218:02, 28 August 2019 diff hist +5 Protein Target Preparation Updated →How Blastermaster works
- 18:0018:00, 28 August 2019 diff hist +1 Protein Target Preparation Updated →How Blastermaster works
- 17:5717:57, 28 August 2019 diff hist −1 Protein Target Preparation Updated →How Blastermaster works
- 17:5617:56, 28 August 2019 diff hist +10 Protein Target Preparation Updated →How Blastermaster works
- 17:5617:56, 28 August 2019 diff hist +11 Protein Target Preparation Updated →How Blastermaster works
- 17:5617:56, 28 August 2019 diff hist +4,888 Protein Target Preparation Updated No edit summary
- 17:0417:04, 28 August 2019 diff hist −2 Protein Target Preparation Updated →Running Blastermaster
- 17:0417:04, 28 August 2019 diff hist +89 Protein Target Preparation Updated →Running Blastermaster
- 17:0317:03, 28 August 2019 diff hist +12 Protein Target Preparation Updated →Running Blastermaster
- 17:0217:02, 28 August 2019 diff hist +327 Protein Target Preparation Updated →Running Blastermaster
- 16:5916:59, 28 August 2019 diff hist +31 Protein Target Preparation Updated No edit summary
- 16:5816:58, 28 August 2019 diff hist +2 Using thin spheres in DOCK3.7 No edit summary
- 16:5716:57, 28 August 2019 diff hist −5,743 Protein Target Preparation →Checking Your Protein Preparation current
- 16:5616:56, 28 August 2019 diff hist +5,671 N Protein Target Preparation Updated Created page with "== Checking Your Protein Preparation == written by Reed Stein, 4/3/2019 === Electrostatics === The electrostatics grid used in docking is called "trim.electrostatics.phi". ..."
- 16:5516:55, 28 August 2019 diff hist +41 DOCK 3.7 →Prepare Receptor
- 16:5316:53, 28 August 2019 diff hist +20 Generating decoys (Reed's way) →Step 1) Setting up SMILES directory
- 16:5316:53, 28 August 2019 diff hist +20 Generating decoys (Reed's way) →Step 1) Setting up directories for Protomers
- 16:4916:49, 28 August 2019 diff hist −2 Generating decoys (Reed's way) →Step 1) Setting up directories for Protomers
- 16:4816:48, 28 August 2019 diff hist −2 Generating decoys (Reed's way) →Step 1) Setting up SMILES directory
- 16:4616:46, 28 August 2019 diff hist −2 Generating decoys (Reed's way) →Step 4) Copying decoy .db2.gz files into your directories
- 16:4516:45, 28 August 2019 diff hist −12 Generating decoys (Reed's way) →Step 3) Assigning accepted protomer decoys to each ligand protomer
- 16:4416:44, 28 August 2019 diff hist −15 Generating decoys (Reed's way) →Step 3) Assigning accepted protomer decoys to each ligand protomer
- 16:4416:44, 28 August 2019 diff hist −19 Generating decoys (Reed's way) →Step 3) Assigning decoys to ligands
- 16:4416:44, 28 August 2019 diff hist +215 Generating decoys (Reed's way) →Step 3) Assigning decoys to ligands
- 16:4316:43, 28 August 2019 diff hist −14 Generating decoys (Reed's way) →Step 4) Setting up ligand/decoy directories for building SMILES
- 16:4316:43, 28 August 2019 diff hist +215 Generating decoys (Reed's way) →Step 3) Assigning accepted protomer decoys to each ligand protomer
- 00:1900:19, 28 August 2019 diff hist +30 Generating decoys (Reed's way) →Step 4) Setting up ligand/decoy directories for building SMILES
23 August 2019
- 23:3623:36, 23 August 2019 diff hist +297 Generating decoys (Reed's way) →Step 4) Setting up ligand/decoy directories for building SMILES
- 21:4021:40, 23 August 2019 diff hist +48 Generating decoys (Reed's way) →Step 1) Setting up SMILES directory
- 21:3921:39, 23 August 2019 diff hist +70 Generating decoys (Reed's way) →Step 4) Copying decoy .db2.gz files into your directories
- 21:3821:38, 23 August 2019 diff hist +101 Generating decoys (Reed's way) →Step 4) Setting up ligand/decoy directories for building SMILES
- 21:3721:37, 23 August 2019 diff hist +423 Generating decoys (Reed's way) →Step 3) Assigning accepted protomer decoys to each ligand protomer
- 21:3621:36, 23 August 2019 diff hist +422 Generating decoys (Reed's way) →Step 3) Assigning decoys to ligands
15 August 2019
- 19:2819:28, 15 August 2019 diff hist +2 Generating decoys (Reed's way) No edit summary
- 19:2819:28, 15 August 2019 diff hist +412 Generating decoys (Reed's way) No edit summary
7 May 2019
- 22:2822:28, 7 May 2019 diff hist +12 Generating decoys (Reed's way) →Step 4) Setting up ligand/decoy directories for building SMILES
4 May 2019
- 02:5802:58, 4 May 2019 diff hist +9 Generating decoys (Reed's way) →Step 1) Setting up directories for Protomers
- 02:5302:53, 4 May 2019 diff hist −58 Generating decoys (Reed's way) No edit summary
- 02:4302:43, 4 May 2019 diff hist −94 Generating decoys (Reed's way) →Step 1) Setting up directories for Protomers
3 May 2019
- 23:3423:34, 3 May 2019 diff hist +4 Generating decoys (Reed's way) No edit summary
- 23:3023:30, 3 May 2019 diff hist +4 Generating decoys (Reed's way) →Step 1) Setting up SMILES directory
- 23:3023:30, 3 May 2019 diff hist +66 Generating decoys (Reed's way) →Step 1) Setting up SMILES directory
- 23:2523:25, 3 May 2019 diff hist +9 Generating decoys (Reed's way) →Step 3) Assigning accepted protomer decoys to each ligand protomer
- 23:2523:25, 3 May 2019 diff hist +738 Generating decoys (Reed's way) →Step 3) Assigning decoys to ligands
- 23:2323:23, 3 May 2019 diff hist +73 Generating decoys (Reed's way) →Step 3) Assigning accepted protomer decoys to each ligand protomer
- 23:2323:23, 3 May 2019 diff hist +93 Generating decoys (Reed's way) →Step 3) Assigning accepted protomer decoys to each ligand protomer
- 23:2123:21, 3 May 2019 diff hist −41 Generating decoys (Reed's way) →Step 3) Assigning decoys to ligands
- 23:2123:21, 3 May 2019 diff hist +15 Generating decoys (Reed's way) →Step 1) Setting up SMILES directory
- 23:2023:20, 3 May 2019 diff hist +4 Generating decoys (Reed's way) →Visualizing decoy Tanimotos to ligands
- 23:2023:20, 3 May 2019 diff hist +4 Generating decoys (Reed's way) →Visualizing property distributions
- 23:1923:19, 3 May 2019 diff hist −33 Generating decoys (Reed's way) →Step 3) Assigning accepted SMILES decoys to ligand protomers
- 23:1923:19, 3 May 2019 diff hist +13 Generating decoys (Reed's way) →Step 3) Removing SMILES decoys that are too similar to known ligands
- 23:1823:18, 3 May 2019 diff hist −9 Generating decoys (Reed's way) →Step 4) Setting up ligand/decoy directories for building SMILES
- 23:1723:17, 3 May 2019 diff hist −600 Generating decoys (Reed's way) No edit summary
- 23:1723:17, 3 May 2019 diff hist −15 Generating decoys (Reed's way) →Step 3) Removing SMILES decoys that are too similar to known ligands
- 23:1723:17, 3 May 2019 diff hist −27 Generating decoys (Reed's way) →Step 2) Retrieving SMILES decoys from ZINC15
- 23:1623:16, 3 May 2019 diff hist +457 Generating decoys (Reed's way) →Step 1) Setting up SMILES directory
- 23:1223:12, 3 May 2019 diff hist +4 Generating decoys (Reed's way) →Step 4) Copying decoy .db2.gz files into your directories
- 23:1123:11, 3 May 2019 diff hist +4 Generating decoys (Reed's way) →Step 3) Assigning accepted protomer decoys to each ligand protomer
- 23:1123:11, 3 May 2019 diff hist +689 Generating decoys (Reed's way) →Step 3) Assigning accepted protomer decoys to each ligand protomer
- 23:0623:06, 3 May 2019 diff hist +136 Generating decoys (Reed's way) →Step 1) Setting up directories for Protomers
- 23:0523:05, 3 May 2019 diff hist 0 Generating decoys (Reed's way) →Step 3) Assigning accepted protomer decoys to each ligand protomer
- 23:0523:05, 3 May 2019 diff hist −344 Generating decoys (Reed's way) No edit summary
- 23:0523:05, 3 May 2019 diff hist −29 Generating decoys (Reed's way) →Step 2) Retrieving protomer decoys from ZINC15
- 23:0423:04, 3 May 2019 diff hist +17 Generating decoys (Reed's way) No edit summary
- 23:0423:04, 3 May 2019 diff hist +165 Generating decoys (Reed's way) →Step 1) Setting up directories for Protomers
22 April 2019
- 18:0918:09, 22 April 2019 diff hist +44 Using thin spheres in DOCK3.7 No edit summary
16 April 2019
- 23:0323:03, 16 April 2019 diff hist +132 Using thin spheres in DOCK3.7 No edit summary
- 22:4622:46, 16 April 2019 diff hist +59 How to do parameter scanning →Blastermaster Parameter Scanning
- 22:4622:46, 16 April 2019 diff hist +162 How to do parameter scanning →Blastermaster Parameter Scanning
- 20:0820:08, 16 April 2019 diff hist +139 Using thin spheres in DOCK3.7 No edit summary
15 April 2019
- 16:5216:52, 15 April 2019 diff hist +7 How to do parameter scanning No edit summary
- 16:5216:52, 15 April 2019 diff hist +12 How to do parameter scanning No edit summary
- 15:5915:59, 15 April 2019 diff hist +117 How to do parameter scanning No edit summary
- 15:5415:54, 15 April 2019 diff hist +1,649 How to do parameter scanning No edit summary
12 April 2019
- 19:0219:02, 12 April 2019 diff hist +92 Adding Static Waters to the Protein Structure No edit summary current
- 19:0019:00, 12 April 2019 diff hist +12 Adding Static Waters to the Protein Structure No edit summary
- 19:0019:00, 12 April 2019 diff hist +155 Adding Static Waters to the Protein Structure No edit summary
4 April 2019
- 18:0918:09, 4 April 2019 diff hist +25 Protein Target Preparation →Ligand Desolvation
- 18:0818:08, 4 April 2019 diff hist +2 Protein Target Preparation →Electrostatics
3 April 2019
- 22:3122:31, 3 April 2019 diff hist +5,645 Protein Target Preparation No edit summary
5 March 2019
- 00:2100:21, 5 March 2019 diff hist +8 Tutorial on running Molecular Dynamics for GIST grid generation →Combining GIST grids current
- 00:2000:20, 5 March 2019 diff hist +286 Tutorial on running Molecular Dynamics for GIST grid generation →Combining GIST grids
4 March 2019
- 18:5318:53, 4 March 2019 diff hist +9 Tutorial on running Molecular Dynamics for GIST grid generation →Run convergence analysis
- 18:5218:52, 4 March 2019 diff hist +221 Tutorial on running Molecular Dynamics for GIST grid generation →Run GIST post processing
28 February 2019
- 21:2121:21, 28 February 2019 diff hist −75 Tutorial on running Molecular Dynamics for GIST grid generation →Run AMBER
25 February 2019
- 20:0120:01, 25 February 2019 diff hist +21 Tutorial on running Molecular Dynamics for GIST grid generation →Run AMBER
- 20:0020:00, 25 February 2019 diff hist +112 Tutorial on running Molecular Dynamics for GIST grid generation →Run AMBER
7 February 2019
- 01:1201:12, 7 February 2019 diff hist +237 Generating decoys (Reed's way) No edit summary
31 October 2018
- 19:0819:08, 31 October 2018 diff hist +386 Generating decoys (Reed's way) →Step 1) Setting up SMILES directory
14 September 2018
- 23:0723:07, 14 September 2018 diff hist +1 Generating decoys (Reed's way) →Step 5) Copying decoy .db2.gz files into your directories
- 23:0723:07, 14 September 2018 diff hist −45 Generating decoys (Reed's way) →Step 5) Copying decoy .db2.gz files into your directories
- 23:0623:06, 14 September 2018 diff hist −7 Generating decoys (Reed's way) →Step 1) Setting up SMILES directories for Protomers
- 21:5621:56, 14 September 2018 diff hist +1 Generating decoys (Reed's way) →Step 1) Setting up SMILES directories for Protomers
- 21:5521:55, 14 September 2018 diff hist +95 Generating decoys (Reed's way) →Step 1) Setting up SMILES directories for Protomers
- 21:5221:52, 14 September 2018 diff hist +2,956 Generating decoys (Reed's way) No edit summary
6 June 2018
- 18:0418:04, 6 June 2018 diff hist +56 DOCK 3.7 tart No edit summary current
5 June 2018
- 18:3818:38, 5 June 2018 diff hist +12 DOCK 3.7 tart →Quick Tarting
25 April 2018
- 23:1323:13, 25 April 2018 diff hist +377 Generating decoys (Reed's way) No edit summary
- 23:1023:10, 25 April 2018 diff hist −100 Generating decoys (Reed's way) →Copying decoy .db2.gz files into your directories
- 23:0523:05, 25 April 2018 diff hist +6 Generating decoys (Reed's way) →Copying decoy .db2.gz files into your directories
- 23:0523:05, 25 April 2018 diff hist +75 Generating decoys (Reed's way) →Copying decoy .db2.gz files into your directories
- 22:5322:53, 25 April 2018 diff hist +366 Generating decoys (Reed's way) →Setting up SMILES directory
19 April 2018
- 00:1000:10, 19 April 2018 diff hist +269 Generating decoys (Reed's way) No edit summary
18 April 2018
- 22:4422:44, 18 April 2018 diff hist +123 Generating decoys (Reed's way) No edit summary
- 20:5820:58, 18 April 2018 diff hist +136 Generating decoys (Reed's way) →Setting up SMILES directory
6 April 2018
- 21:1921:19, 6 April 2018 diff hist +377 Generating decoys (Reed's way) No edit summary
- 18:0618:06, 6 April 2018 diff hist +1 Generating decoys (Reed's way) →Setting up SMILES directory
- 18:0518:05, 6 April 2018 diff hist +2 Generating decoys (Reed's way) →Setting up SMILES directory
- 18:0318:03, 6 April 2018 diff hist +1 Generating decoys (Reed's way) →Setting up SMILES directory
- 16:2616:26, 6 April 2018 diff hist −196 Generating decoys (Reed's way) No edit summary
- 00:1100:11, 6 April 2018 diff hist −2 Generating decoys (Reed's way) →Retrieving decoys from ZINC15
- 00:1100:11, 6 April 2018 diff hist +15 Generating decoys (Reed's way) →Retrieving decoys from ZINC15
- 00:0400:04, 6 April 2018 diff hist +107 Generating decoys (Reed's way) →Assigning accepted decoys to each ligand protomer
- 00:0100:01, 6 April 2018 diff hist −113 Generating decoys (Reed's way) →Assigning accepted decoys to each ligand protomer
5 April 2018
- 22:0222:02, 5 April 2018 diff hist +157 Generating decoys (Reed's way) →Retrieving decoys from ZINC15
4 April 2018
- 23:3823:38, 4 April 2018 diff hist +466 Generating decoys (Reed's way) No edit summary
- 21:3421:34, 4 April 2018 diff hist −2 Generating decoys (Reed's way) →Copying decoy .db2.gz files into your directories
- 21:3421:34, 4 April 2018 diff hist 0 Generating decoys (Reed's way) →Retrieving Decoys from ZINC15
- 21:3321:33, 4 April 2018 diff hist 0 Generating decoys (Reed's way) →Removing Decoys that are too similar to known ligands
- 21:0621:06, 4 April 2018 diff hist +1 Generating decoys (Reed's way) →Retrieving Decoys from ZINC15
- 21:0321:03, 4 April 2018 diff hist +213 Generating decoys (Reed's way) →Assigning accepted decoys to each ligand protomer
- 21:0221:02, 4 April 2018 diff hist +266 Generating decoys (Reed's way) →Retrieving Decoys from ZINC15
3 April 2018
- 21:1721:17, 3 April 2018 diff hist +3,430 N Generating decoys (Reed's way) Created page with "Written on April 3, 2018. All scripts for this tutorial can be found in: /mnt/nfs/home/rstein/zzz.scripts/DUDE_SCRIPTS/ == Input SMILES file == Starting with a SMILES f..."
- 20:4720:47, 3 April 2018 diff hist +37 DOCK 3.7 →Prepare Screening Library
12 December 2017
- 23:3723:37, 12 December 2017 diff hist +30 DOCK 3.7 tart No edit summary
- 23:3623:36, 12 December 2017 diff hist +10 DOCK 3.7 tart No edit summary
- 23:3623:36, 12 December 2017 diff hist −5 DOCK 3.7 tart No edit summary
- 23:3523:35, 12 December 2017 diff hist +1,085 DOCK 3.7 tart No edit summary