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- 18:02, 29 May 2020 diff hist +2 How to do parameter scanning
- 18:02, 29 May 2020 diff hist +190 How to do parameter scanning
- 17:51, 29 May 2020 diff hist +28 How to do parameter scanning
- 17:50, 29 May 2020 diff hist 0 How to do parameter scanning
- 20:17, 27 May 2020 diff hist +79 Removing Spheres (The Chase Method) current
- 20:17, 27 May 2020 diff hist -53 Removing Spheres (The Chase Method)
- 19:27, 27 May 2020 diff hist +56 Removing Spheres (The Chase Method)
- 17:13, 27 May 2020 diff hist 0 Generating extrema set current
- 17:12, 27 May 2020 diff hist +141 Generating extrema set
- 20:47, 21 May 2020 diff hist +87 Generating extrema set
- 19:41, 21 May 2020 diff hist +66 Generating extrema set
- 19:40, 21 May 2020 diff hist +89 Generating extrema set
- 19:38, 21 May 2020 diff hist +601 Generating extrema set
- 19:32, 21 May 2020 diff hist -2 How to do parameter scanning →Manually Generating ES/LD Combinations
- 19:32, 21 May 2020 diff hist +2 How to do parameter scanning
- 19:31, 21 May 2020 diff hist +35 DOCK 3.7 →Prepare Receptor
- 19:31, 21 May 2020 diff hist -8 How to do parameter scanning →Blastermaster Parameter Scanning
- 19:31, 21 May 2020 diff hist +36 How to do parameter scanning →Blastermaster Parameter Scanning
- 19:29, 21 May 2020 diff hist +82 How to do parameter scanning →Manually Generating ES/LD Combinations
- 19:27, 21 May 2020 diff hist +293 How to do parameter scanning →Manually Generating ES/LD Combinations
- 19:19, 21 May 2020 diff hist 0 Matching Sphere Scan current
- 19:18, 21 May 2020 diff hist +50 Matching Sphere Scan
- 18:51, 21 May 2020 diff hist +30 Removing Spheres (The Chase Method)
- 18:51, 21 May 2020 diff hist -1 Removing Spheres (The Chase Method)
- 18:50, 21 May 2020 diff hist -1 Removing Spheres (The Chase Method)
- 18:49, 21 May 2020 diff hist +108 Removing Spheres (The Chase Method)
- 18:41, 21 May 2020 diff hist -6 Removing Spheres (The Chase Method)
- 18:40, 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 ..."
- 18:24, 21 May 2020 diff hist +41 DOCK 3.7 →Prepare Receptor
- 01:23, 19 May 2020 diff hist +445 Generating decoys (Reed's way)
- 19:18, 15 May 2020 diff hist -18 Generating decoys (DUDE-Z) Blanked the page current
- 19:18, 15 May 2020 diff hist -40 Blah Blanked the page current
- 19:18, 15 May 2020 diff hist -13,662 Generating Decoys (DUDE-Z) Blanked the page current
- 19:17, 15 May 2020 diff hist +4 DOCK 3.7 →Prepare Screening Library
- 19:15, 15 May 2020 diff hist +40 N Blah Rstein moved page Blah to Generating Decoys (DUDE-Z)
- 19:15, 15 May 2020 diff hist 0 m Generating Decoys (DUDE-Z) Rstein moved page Blah to Generating Decoys (DUDE-Z)
- 19:14, 15 May 2020 diff hist +18 N Generating decoys (DUDE-Z) Rstein moved page Generating decoys (DUDE-Z) to Blah
- 19:14, 15 May 2020 diff hist 0 m Generating Decoys (DUDE-Z) Rstein moved page Generating decoys (DUDE-Z) to Blah
- 18:59, 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...."
- 18:58, 15 May 2020 diff hist -4 DOCK 3.7 →Prepare Screening Library
- 18:07, 15 May 2020 diff hist -29 Matching Sphere Scan
- 18:05, 15 May 2020 diff hist +14 Matching Sphere Scan
- 18:04, 15 May 2020 diff hist +12 Matching Sphere Scan
- 18:03, 15 May 2020 diff hist -1 Matching Sphere Scan
- 18:03, 15 May 2020 diff hist +242 Matching Sphere Scan
- 18:00, 15 May 2020 diff hist +41 Matching Sphere Scan
- 17:58, 15 May 2020 diff hist +52 Matching Sphere Scan
- 17:57, 15 May 2020 diff hist -1 Matching Sphere Scan
- 17:57, 15 May 2020 diff hist +511 Matching Sphere Scan
- 17:48, 15 May 2020 diff hist +99 Matching Sphere Scan
- 17:47, 15 May 2020 diff hist -1 Matching Sphere Scan
- 17:47, 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..."
- 17:44, 15 May 2020 diff hist +26 DOCK 3.7 →Prepare Receptor
- 21:15, 24 March 2020 diff hist +265 Generating decoys (Reed's way) →Querying ZINC for SMILES
- 21:12, 24 March 2020 diff hist +122 Generating decoys (Reed's way) →Querying ZINC for Protomers
- 02:03, 11 March 2020 diff hist +18 Generating decoys (Reed's way)
- 01:59, 11 March 2020 diff hist -3 Generating decoys (Reed's way) →Querying ZINC for SMILES
- 01:51, 11 March 2020 diff hist +13 Generating decoys (Reed's way) →Step 1) Setting up SMILES directory
- 01:51, 11 March 2020 diff hist +13 Generating decoys (Reed's way) →Step 1) Setting up directories for Protomers
- 01:50, 11 March 2020 diff hist -9 Generating decoys (Reed's way) →Step 3) Assigning accepted protomer decoys to each ligand protomer
- 01:49, 11 March 2020 diff hist -9 Generating decoys (Reed's way) →Step 3) Assigning decoys to ligands
- 23:28, 6 March 2020 diff hist +29 Generating decoys (Reed's way) →Step 1) Setting up SMILES directory
- 23:28, 6 March 2020 diff hist +29 Generating decoys (Reed's way) →Step 1) Setting up directories for Protomers
- 19:39, 30 October 2019 diff hist 0 Converting SMILES to Kekule Format current
- 21:11, 17 October 2019 diff hist +237 Converting SMILES to Kekule Format
- 21:04, 17 October 2019 diff hist -8 Converting SMILES to Kekule Format
- 21:04, 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..."
- 21:02, 17 October 2019 diff hist +41 DOCK 3.7 →Analysis
- 00:57, 11 October 2019 diff hist -3 Generating decoys (Reed's way) →Querying ZINC for SMILES
- 00:56, 11 October 2019 diff hist -3 Generating decoys (Reed's way) →Step 1) Setting up directories for Protomers
- 18:59, 10 October 2019 diff hist +535 Protein Target Preparation Updated →Running Blastermaster current
- 02:10, 4 October 2019 diff hist +25 Protein Target Preparation Updated →Running Blastermaster
- 17:31, 3 October 2019 diff hist +105 Protein Target Preparation Updated →Useful References
- 17:28, 3 October 2019 diff hist +11 Protein Target Preparation Updated →Running Blastermaster
- 17:28, 3 October 2019 diff hist +144 Protein Target Preparation Updated →Running Blastermaster
- 17:26, 3 October 2019 diff hist +14 Protein Target Preparation Updated →Running Blastermaster
- 17:24, 3 October 2019 diff hist +6 Protein Target Preparation Updated →Useful References
- 17:24, 3 October 2019 diff hist +1,606 Protein Target Preparation Updated
- 17:09, 3 October 2019 diff hist -3 Protein Target Preparation Updated →Running Blastermaster
- 17:08, 3 October 2019 diff hist +274 Protein Target Preparation Updated →Running Blastermaster
- 17:00, 3 October 2019 diff hist +596 Protein Target Preparation Updated →Running Blastermaster
- 21:38, 28 August 2019 diff hist +1,692 Protein Target Preparation Updated →How Blastermaster works
- 21:30, 28 August 2019 diff hist +74 Protein Target Preparation Updated →How Blastermaster works
- 21:29, 28 August 2019 diff hist +251 Protein Target Preparation Updated →How Blastermaster works
- 19:21, 28 August 2019 diff hist 0 Protein Target Preparation Updated →How Blastermaster works
- 19:20, 28 August 2019 diff hist +67 Protein Target Preparation Updated →How Blastermaster works
- 19:18, 28 August 2019 diff hist +21 Protein Target Preparation Updated →How Blastermaster works
- 19:18, 28 August 2019 diff hist +50 Protein Target Preparation Updated →How Blastermaster works
- 19:17, 28 August 2019 diff hist +373 Protein Target Preparation Updated →How Blastermaster works
- 18:02, 28 August 2019 diff hist +5 Protein Target Preparation Updated →How Blastermaster works
- 18:00, 28 August 2019 diff hist +1 Protein Target Preparation Updated →How Blastermaster works
- 17:57, 28 August 2019 diff hist -1 Protein Target Preparation Updated →How Blastermaster works
- 17:56, 28 August 2019 diff hist +10 Protein Target Preparation Updated →How Blastermaster works
- 17:56, 28 August 2019 diff hist +11 Protein Target Preparation Updated →How Blastermaster works
- 17:56, 28 August 2019 diff hist +4,888 Protein Target Preparation Updated
- 17:04, 28 August 2019 diff hist -2 Protein Target Preparation Updated →Running Blastermaster
- 17:04, 28 August 2019 diff hist +89 Protein Target Preparation Updated →Running Blastermaster
- 17:03, 28 August 2019 diff hist +12 Protein Target Preparation Updated →Running Blastermaster
- 17:02, 28 August 2019 diff hist +327 Protein Target Preparation Updated →Running Blastermaster
- 16:59, 28 August 2019 diff hist +31 Protein Target Preparation Updated
- 16:58, 28 August 2019 diff hist +2 Using thin spheres in DOCK3.7
- 16:57, 28 August 2019 diff hist -5,743 Protein Target Preparation →Checking Your Protein Preparation current
- 16:56, 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". ..."
- 16:55, 28 August 2019 diff hist +41 DOCK 3.7 →Prepare Receptor
- 16:53, 28 August 2019 diff hist +20 Generating decoys (Reed's way) →Step 1) Setting up SMILES directory
- 16:53, 28 August 2019 diff hist +20 Generating decoys (Reed's way) →Step 1) Setting up directories for Protomers
- 16:49, 28 August 2019 diff hist -2 Generating decoys (Reed's way) →Step 1) Setting up directories for Protomers
- 16:48, 28 August 2019 diff hist -2 Generating decoys (Reed's way) →Step 1) Setting up SMILES directory
- 16:46, 28 August 2019 diff hist -2 Generating decoys (Reed's way) →Step 4) Copying decoy .db2.gz files into your directories
- 16:45, 28 August 2019 diff hist -12 Generating decoys (Reed's way) →Step 3) Assigning accepted protomer decoys to each ligand protomer
- 16:44, 28 August 2019 diff hist -15 Generating decoys (Reed's way) →Step 3) Assigning accepted protomer decoys to each ligand protomer
- 16:44, 28 August 2019 diff hist -19 Generating decoys (Reed's way) →Step 3) Assigning decoys to ligands
- 16:44, 28 August 2019 diff hist +215 Generating decoys (Reed's way) →Step 3) Assigning decoys to ligands
- 16:43, 28 August 2019 diff hist -14 Generating decoys (Reed's way) →Step 4) Setting up ligand/decoy directories for building SMILES
- 16:43, 28 August 2019 diff hist +215 Generating decoys (Reed's way) →Step 3) Assigning accepted protomer decoys to each ligand protomer
- 00:19, 28 August 2019 diff hist +30 Generating decoys (Reed's way) →Step 4) Setting up ligand/decoy directories for building SMILES
- 23:36, 23 August 2019 diff hist +297 Generating decoys (Reed's way) →Step 4) Setting up ligand/decoy directories for building SMILES
- 21:40, 23 August 2019 diff hist +48 Generating decoys (Reed's way) →Step 1) Setting up SMILES directory
- 21:39, 23 August 2019 diff hist +70 Generating decoys (Reed's way) →Step 4) Copying decoy .db2.gz files into your directories
- 21:38, 23 August 2019 diff hist +101 Generating decoys (Reed's way) →Step 4) Setting up ligand/decoy directories for building SMILES
- 21:37, 23 August 2019 diff hist +423 Generating decoys (Reed's way) →Step 3) Assigning accepted protomer decoys to each ligand protomer
- 21:36, 23 August 2019 diff hist +422 Generating decoys (Reed's way) →Step 3) Assigning decoys to ligands
- 19:28, 15 August 2019 diff hist +2 Generating decoys (Reed's way)
- 19:28, 15 August 2019 diff hist +412 Generating decoys (Reed's way)
- 22:28, 7 May 2019 diff hist +12 Generating decoys (Reed's way) →Step 4) Setting up ligand/decoy directories for building SMILES
- 02:58, 4 May 2019 diff hist +9 Generating decoys (Reed's way) →Step 1) Setting up directories for Protomers
- 02:53, 4 May 2019 diff hist -58 Generating decoys (Reed's way)
- 02:43, 4 May 2019 diff hist -94 Generating decoys (Reed's way) →Step 1) Setting up directories for Protomers
- 23:34, 3 May 2019 diff hist +4 Generating decoys (Reed's way)
- 23:30, 3 May 2019 diff hist +4 Generating decoys (Reed's way) →Step 1) Setting up SMILES directory
- 23:30, 3 May 2019 diff hist +66 Generating decoys (Reed's way) →Step 1) Setting up SMILES directory
- 23:25, 3 May 2019 diff hist +9 Generating decoys (Reed's way) →Step 3) Assigning accepted protomer decoys to each ligand protomer
- 23:25, 3 May 2019 diff hist +738 Generating decoys (Reed's way) →Step 3) Assigning decoys to ligands
- 23:23, 3 May 2019 diff hist +73 Generating decoys (Reed's way) →Step 3) Assigning accepted protomer decoys to each ligand protomer
- 23:23, 3 May 2019 diff hist +93 Generating decoys (Reed's way) →Step 3) Assigning accepted protomer decoys to each ligand protomer
- 23:21, 3 May 2019 diff hist -41 Generating decoys (Reed's way) →Step 3) Assigning decoys to ligands
- 23:21, 3 May 2019 diff hist +15 Generating decoys (Reed's way) →Step 1) Setting up SMILES directory
- 23:20, 3 May 2019 diff hist +4 Generating decoys (Reed's way) →Visualizing decoy Tanimotos to ligands
- 23:20, 3 May 2019 diff hist +4 Generating decoys (Reed's way) →Visualizing property distributions
- 23:19, 3 May 2019 diff hist -33 Generating decoys (Reed's way) →Step 3) Assigning accepted SMILES decoys to ligand protomers
- 23:19, 3 May 2019 diff hist +13 Generating decoys (Reed's way) →Step 3) Removing SMILES decoys that are too similar to known ligands
- 23:18, 3 May 2019 diff hist -9 Generating decoys (Reed's way) →Step 4) Setting up ligand/decoy directories for building SMILES
- 23:17, 3 May 2019 diff hist -600 Generating decoys (Reed's way)
- 23:17, 3 May 2019 diff hist -15 Generating decoys (Reed's way) →Step 3) Removing SMILES decoys that are too similar to known ligands
- 23:17, 3 May 2019 diff hist -27 Generating decoys (Reed's way) →Step 2) Retrieving SMILES decoys from ZINC15
- 23:16, 3 May 2019 diff hist +457 Generating decoys (Reed's way) →Step 1) Setting up SMILES directory
- 23:12, 3 May 2019 diff hist +4 Generating decoys (Reed's way) →Step 4) Copying decoy .db2.gz files into your directories
- 23:11, 3 May 2019 diff hist +4 Generating decoys (Reed's way) →Step 3) Assigning accepted protomer decoys to each ligand protomer
- 23:11, 3 May 2019 diff hist +689 Generating decoys (Reed's way) →Step 3) Assigning accepted protomer decoys to each ligand protomer
- 23:06, 3 May 2019 diff hist +136 Generating decoys (Reed's way) →Step 1) Setting up directories for Protomers
- 23:05, 3 May 2019 diff hist 0 Generating decoys (Reed's way) →Step 3) Assigning accepted protomer decoys to each ligand protomer
- 23:05, 3 May 2019 diff hist -344 Generating decoys (Reed's way)
- 23:05, 3 May 2019 diff hist -29 Generating decoys (Reed's way) →Step 2) Retrieving protomer decoys from ZINC15
- 23:04, 3 May 2019 diff hist +17 Generating decoys (Reed's way)
- 23:04, 3 May 2019 diff hist +165 Generating decoys (Reed's way) →Step 1) Setting up directories for Protomers
- 18:09, 22 April 2019 diff hist +44 Using thin spheres in DOCK3.7
- 23:03, 16 April 2019 diff hist +132 Using thin spheres in DOCK3.7
- 22:46, 16 April 2019 diff hist +59 How to do parameter scanning →Blastermaster Parameter Scanning
- 22:46, 16 April 2019 diff hist +162 How to do parameter scanning →Blastermaster Parameter Scanning
- 20:08, 16 April 2019 diff hist +139 Using thin spheres in DOCK3.7
- 16:52, 15 April 2019 diff hist +7 How to do parameter scanning
- 16:52, 15 April 2019 diff hist +12 How to do parameter scanning
- 15:59, 15 April 2019 diff hist +117 How to do parameter scanning
- 15:54, 15 April 2019 diff hist +1,649 How to do parameter scanning
- 19:02, 12 April 2019 diff hist +92 Adding Static Waters to the Protein Structure current
- 19:00, 12 April 2019 diff hist +12 Adding Static Waters to the Protein Structure
- 19:00, 12 April 2019 diff hist +155 Adding Static Waters to the Protein Structure
- 18:09, 4 April 2019 diff hist +25 Protein Target Preparation →Ligand Desolvation
- 18:08, 4 April 2019 diff hist +2 Protein Target Preparation →Electrostatics
- 22:31, 3 April 2019 diff hist +5,645 Protein Target Preparation
- 00:21, 5 March 2019 diff hist +8 Tutorial on running Molecular Dynamics for GIST grid generation →Combining GIST grids current
- 00:20, 5 March 2019 diff hist +286 Tutorial on running Molecular Dynamics for GIST grid generation →Combining GIST grids
- 18:53, 4 March 2019 diff hist +9 Tutorial on running Molecular Dynamics for GIST grid generation →Run convergence analysis
- 18:52, 4 March 2019 diff hist +221 Tutorial on running Molecular Dynamics for GIST grid generation →Run GIST post processing
- 21:21, 28 February 2019 diff hist -75 Tutorial on running Molecular Dynamics for GIST grid generation →Run AMBER
- 20:01, 25 February 2019 diff hist +21 Tutorial on running Molecular Dynamics for GIST grid generation →Run AMBER
- 20:00, 25 February 2019 diff hist +112 Tutorial on running Molecular Dynamics for GIST grid generation →Run AMBER
- 01:12, 7 February 2019 diff hist +237 Generating decoys (Reed's way)
- 19:08, 31 October 2018 diff hist +386 Generating decoys (Reed's way) →Step 1) Setting up SMILES directory
- 23:07, 14 September 2018 diff hist +1 Generating decoys (Reed's way) →Step 5) Copying decoy .db2.gz files into your directories
- 23:07, 14 September 2018 diff hist -45 Generating decoys (Reed's way) →Step 5) Copying decoy .db2.gz files into your directories
- 23:06, 14 September 2018 diff hist -7 Generating decoys (Reed's way) →Step 1) Setting up SMILES directories for Protomers
- 21:56, 14 September 2018 diff hist +1 Generating decoys (Reed's way) →Step 1) Setting up SMILES directories for Protomers
- 21:55, 14 September 2018 diff hist +95 Generating decoys (Reed's way) →Step 1) Setting up SMILES directories for Protomers
- 21:52, 14 September 2018 diff hist +2,956 Generating decoys (Reed's way)
- 18:04, 6 June 2018 diff hist +56 DOCK 3.7 tart current
- 18:38, 5 June 2018 diff hist +12 DOCK 3.7 tart →Quick Tarting
- 23:13, 25 April 2018 diff hist +377 Generating decoys (Reed's way)
- 23:10, 25 April 2018 diff hist -100 Generating decoys (Reed's way) →Copying decoy .db2.gz files into your directories
- 23:05, 25 April 2018 diff hist +6 Generating decoys (Reed's way) →Copying decoy .db2.gz files into your directories
- 23:05, 25 April 2018 diff hist +75 Generating decoys (Reed's way) →Copying decoy .db2.gz files into your directories
- 22:53, 25 April 2018 diff hist +366 Generating decoys (Reed's way) →Setting up SMILES directory
- 00:10, 19 April 2018 diff hist +269 Generating decoys (Reed's way)
- 22:44, 18 April 2018 diff hist +123 Generating decoys (Reed's way)
- 20:58, 18 April 2018 diff hist +136 Generating decoys (Reed's way) →Setting up SMILES directory
- 21:19, 6 April 2018 diff hist +377 Generating decoys (Reed's way)
- 18:06, 6 April 2018 diff hist +1 Generating decoys (Reed's way) →Setting up SMILES directory
- 18:05, 6 April 2018 diff hist +2 Generating decoys (Reed's way) →Setting up SMILES directory
- 18:03, 6 April 2018 diff hist +1 Generating decoys (Reed's way) →Setting up SMILES directory
- 16:26, 6 April 2018 diff hist -196 Generating decoys (Reed's way)
- 00:11, 6 April 2018 diff hist -2 Generating decoys (Reed's way) →Retrieving decoys from ZINC15
- 00:11, 6 April 2018 diff hist +15 Generating decoys (Reed's way) →Retrieving decoys from ZINC15
- 00:04, 6 April 2018 diff hist +107 Generating decoys (Reed's way) →Assigning accepted decoys to each ligand protomer
- 00:01, 6 April 2018 diff hist -113 Generating decoys (Reed's way) →Assigning accepted decoys to each ligand protomer
- 22:02, 5 April 2018 diff hist +157 Generating decoys (Reed's way) →Retrieving decoys from ZINC15
- 23:38, 4 April 2018 diff hist +466 Generating decoys (Reed's way)
- 21:34, 4 April 2018 diff hist -2 Generating decoys (Reed's way) →Copying decoy .db2.gz files into your directories
- 21:34, 4 April 2018 diff hist 0 Generating decoys (Reed's way) →Retrieving Decoys from ZINC15
- 21:33, 4 April 2018 diff hist 0 Generating decoys (Reed's way) →Removing Decoys that are too similar to known ligands
- 21:06, 4 April 2018 diff hist +1 Generating decoys (Reed's way) →Retrieving Decoys from ZINC15
- 21:03, 4 April 2018 diff hist +213 Generating decoys (Reed's way) →Assigning accepted decoys to each ligand protomer
- 21:02, 4 April 2018 diff hist +266 Generating decoys (Reed's way) →Retrieving Decoys from ZINC15
- 21:17, 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..."
- 20:47, 3 April 2018 diff hist +37 DOCK 3.7 →Prepare Screening Library
- 23:37, 12 December 2017 diff hist +30 DOCK 3.7 tart
- 23:36, 12 December 2017 diff hist +10 DOCK 3.7 tart
- 23:36, 12 December 2017 diff hist -5 DOCK 3.7 tart
- 23:35, 12 December 2017 diff hist +1,085 DOCK 3.7 tart