User contributions for Rstein
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21 May 2020
- 19:1919:19, 21 May 2020 diff hist 0 Matching Sphere Scan No edit summary current
- 19:1819:18, 21 May 2020 diff hist +50 Matching Sphere Scan No edit summary
- 18:5118:51, 21 May 2020 diff hist +30 Removing Spheres (The Chase Method) No edit summary
- 18:5118:51, 21 May 2020 diff hist −1 Removing Spheres (The Chase Method) No edit summary
- 18:5018:50, 21 May 2020 diff hist −1 Removing Spheres (The Chase Method) No edit summary
- 18:4918:49, 21 May 2020 diff hist +108 Removing Spheres (The Chase Method) No edit summary
- 18:4118:41, 21 May 2020 diff hist −6 Removing Spheres (The Chase Method) No edit summary
- 18:4018:40, 21 May 2020 diff hist +2,343 N Removing Spheres (The Chase Method) Created page with "These scripts are used for removing ligand desolvation spheres around atom(s) of interest. This is to decrease the desolvation cost in a targeted way. 5/21/2020 Pioneered by ..."
- 18:2418:24, 21 May 2020 diff hist +41 DOCK 3.7 →Prepare Receptor
19 May 2020
- 01:2301:23, 19 May 2020 diff hist +445 Generating decoys (Reed's way) No edit summary
15 May 2020
- 19:1819:18, 15 May 2020 diff hist −18 Generating decoys (DUDE-Z) Blanked the page current
- 19:1819:18, 15 May 2020 diff hist −40 Blah Blanked the page current
- 19:1819:18, 15 May 2020 diff hist −13,662 Generating Decoys (DUDE-Z) Blanked the page
- 19:1719:17, 15 May 2020 diff hist +4 DOCK 3.7 →Prepare Screening Library
- 19:1519:15, 15 May 2020 diff hist +40 N Blah Rstein moved page Blah to Generating Decoys (DUDE-Z)
- 19:1519:15, 15 May 2020 diff hist 0 m Generating Decoys (DUDE-Z) Rstein moved page Blah to Generating Decoys (DUDE-Z)
- 19:1419:14, 15 May 2020 diff hist +18 N Generating decoys (DUDE-Z) Rstein moved page Generating decoys (DUDE-Z) to Blah
- 19:1419:14, 15 May 2020 diff hist 0 m Generating Decoys (DUDE-Z) Rstein moved page Generating decoys (DUDE-Z) to Blah
- 18:5918:59, 15 May 2020 diff hist +13,662 N Generating Decoys (DUDE-Z) Created page with "Written by Reed Stein on April 3, 2018. updated 5/3/2019 updated 8/15/2019 updated 3/6/2020 This pipeline will generate property-matched decoys for a set of ligand SMILES...."
- 18:5818:58, 15 May 2020 diff hist −4 DOCK 3.7 →Prepare Screening Library
- 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