User contributions for Jklyu
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31 March 2021
- 19:0919:09, 31 March 2021 diff hist +1,356 Coloring and Subcluster Matching No edit summary
- 19:0619:06, 31 March 2021 diff hist −1 Coloring and Subcluster Matching No edit summary
- 19:0419:04, 31 March 2021 diff hist 0 Coloring and Subcluster Matching No edit summary
- 19:0419:04, 31 March 2021 diff hist +337 Coloring and Subcluster Matching No edit summary
- 18:5418:54, 31 March 2021 diff hist −15 Coloring and Subcluster Matching No edit summary
- 18:5418:54, 31 March 2021 diff hist +58 Coloring and Subcluster Matching No edit summary
- 18:5018:50, 31 March 2021 diff hist +296 Coloring and Subcluster Matching No edit summary
- 18:4818:48, 31 March 2021 diff hist +226 Coloring and Subcluster Matching No edit summary
- 18:3018:30, 31 March 2021 diff hist +70 Coloring and Subcluster Matching No edit summary
- 18:1318:13, 31 March 2021 diff hist +44 Coloring and Subcluster Matching No edit summary
- 18:1218:12, 31 March 2021 diff hist +107 Coloring and Subcluster Matching No edit summary
- 18:0918:09, 31 March 2021 diff hist +92 Coloring and Subcluster Matching No edit summary
- 18:0318:03, 31 March 2021 diff hist +43 N Coloring and Subcluster Matching Created page with "Written by Jiankun Lyu on March 31st, 2021."
- 17:2917:29, 31 March 2021 diff hist +39 DOCK 3.7 No edit summary
15 November 2019
- 21:5421:54, 15 November 2019 diff hist +131 Generating decoys (Reed's way) →Step 4) Setting up ligand/decoy directories for building SMILES
12 October 2019
- 21:4921:49, 12 October 2019 diff hist +231 Generating extrema set No edit summary
- 21:3821:38, 12 October 2019 diff hist +7 Generating extrema set No edit summary
- 21:3821:38, 12 October 2019 diff hist 0 Generating extrema set No edit summary
- 21:3421:34, 12 October 2019 diff hist +299 Generating extrema set No edit summary
- 21:3021:30, 12 October 2019 diff hist +378 Generating extrema set No edit summary
- 21:2521:25, 12 October 2019 diff hist +175 Generating extrema set No edit summary
- 21:2121:21, 12 October 2019 diff hist +695 Generating extrema set No edit summary
- 21:1821:18, 12 October 2019 diff hist +293 Generating extrema set No edit summary
- 21:1521:15, 12 October 2019 diff hist +33 Generating extrema set No edit summary
- 21:1421:14, 12 October 2019 diff hist 0 N File:Download.png No edit summary current
- 21:1321:13, 12 October 2019 diff hist +180 Generating extrema set No edit summary
- 21:1321:13, 12 October 2019 diff hist 0 N File:Plus2.png No edit summary current
- 21:1221:12, 12 October 2019 diff hist 0 N File:Plus1.png No edit summary current
- 21:1221:12, 12 October 2019 diff hist +220 Generating extrema set No edit summary
- 21:1121:11, 12 October 2019 diff hist 0 N File:0.png No edit summary current
- 21:1021:10, 12 October 2019 diff hist 0 N File:Minus1.png No edit summary current
- 21:0621:06, 12 October 2019 diff hist +22 Generating extrema set No edit summary
- 21:0321:03, 12 October 2019 diff hist +29 N File:Minus2.png extrema_set_goldilocks_minus2 current
- 21:0221:02, 12 October 2019 diff hist +388 Generating extrema set No edit summary
- 19:2119:21, 12 October 2019 diff hist +949 N Generating extrema set Created page with "Written by Jiankun Lyu, 2019/10/12 extrema_set_gen------- working | |------ ZINC-downloader-3D-smi.database_..."
- 19:0919:09, 12 October 2019 diff hist +29 DOCK 3.7 No edit summary
5 August 2019
19 March 2019
- 18:1918:19, 19 March 2019 diff hist 0 Bemis-Murcko Scaffold Analysis No edit summary current
15 March 2019
- 23:2023:20, 15 March 2019 diff hist +1 March2019 protocol No edit summary
- 18:4918:49, 15 March 2019 diff hist −24 Filtering ligands for novelty No edit summary current
9 June 2018
- 20:2520:25, 9 June 2018 diff hist +45 Whole Library TC to Knowns Calculations No edit summary current
24 May 2018
- 20:4720:47, 24 May 2018 diff hist +245 Whole Library TC to Knowns Calculations No edit summary
- 20:4320:43, 24 May 2018 diff hist +292 Whole Library TC to Knowns Calculations No edit summary
- 20:2720:27, 24 May 2018 diff hist +583 Whole Library TC to Knowns Calculations No edit summary
- 20:2020:20, 24 May 2018 diff hist +326 Whole Library TC to Knowns Calculations No edit summary
- 19:5319:53, 24 May 2018 diff hist +814 Whole Library TC to Knowns Calculations No edit summary
- 17:0117:01, 24 May 2018 diff hist +32 N Whole Library TC to Knowns Calculations Created page with "Written by Jiankun Lyu, 20180524"
- 16:5916:59, 24 May 2018 diff hist +46 DOCK 3.7 →Post Docking Filters
9 March 2018
- 23:1123:11, 9 March 2018 diff hist +1 Visualize docking grids No edit summary current
- 23:1023:10, 9 March 2018 diff hist +65 Visualize docking grids No edit summary
- 23:0923:09, 9 March 2018 diff hist +253 Visualize docking grids No edit summary
- 23:0423:04, 9 March 2018 diff hist +347 Visualize docking grids No edit summary
- 22:5722:57, 9 March 2018 diff hist +195 N Visualize docking grids Created page with "Written by Jiankun Lyu, 20180309 1) Convert grids into a format that Chimera can read in 1.1) The vdw grid 1.2) The electrostatic grid 1.3) The desolvation grid 2) Visual..."
- 22:5222:52, 9 March 2018 diff hist +30 DOCK 3.7 →Prepare Receptor
7 March 2018
- 21:3521:35, 7 March 2018 diff hist +170 TC analog searching in ZINC No edit summary
- 21:3221:32, 7 March 2018 diff hist +548 N TC analog searching in ZINC Created page with "Written by Jiankun Lyu, 2018/03/07 1) Create a directory for your searching results. mkdir tc_analog_searching cd tc_analog_searching 2) Create a file that contains ZINC I..."
- 21:2521:25, 7 March 2018 diff hist +7 DOCK 3.7 →Analog by Catalog
- 21:2321:23, 7 March 2018 diff hist +27 DOCK 3.7 →Analog by Catalog
1 December 2017
- 22:3322:33, 1 December 2017 diff hist +4 How to process results from a large-scale docking →Cluster results
24 October 2017
- 22:4822:48, 24 October 2017 diff hist −41 How to process results from a large-scale docking →Get poses of cluster heads
- 22:4722:47, 24 October 2017 diff hist +269 How to process results from a large-scale docking →Get poses of cluster heads
- 22:4422:44, 24 October 2017 diff hist −22 How to process results from a large-scale docking →Get poses of cluster heads
- 22:4322:43, 24 October 2017 diff hist +345 How to process results from a large-scale docking No edit summary
- 22:4122:41, 24 October 2017 diff hist +383 How to process results from a large-scale docking →Cluster results
- 22:4022:40, 24 October 2017 diff hist +5 How to process results from a large-scale docking →Cluster results
18 October 2017
- 22:0422:04, 18 October 2017 diff hist −7 How to process results from a large-scale docking →Combine results
- 19:5919:59, 18 October 2017 diff hist +241 How to process results from a large-scale docking →Check for completion and resubmit failed jobs
- 19:0119:01, 18 October 2017 diff hist 0 How to process results from a large-scale docking No edit summary
- 18:5618:56, 18 October 2017 diff hist +161 How to process results from a large-scale docking No edit summary
- 18:4918:49, 18 October 2017 diff hist +219 How to process results from a large-scale docking No edit summary
- 18:3118:31, 18 October 2017 diff hist +586 N How to process results from a large-scale docking Created page with "Written by Jiankun Lyu, 20171018 == Check for completion and resubmit failed jobs == In a large calculation such as this one with tens of thousands of separate processes, it..."
- 18:1118:11, 18 October 2017 diff hist +2 DOCK 3.7 →Post Docking Clustering
- 18:1118:11, 18 October 2017 diff hist +55 DOCK 3.7 →Post Docking Clustering
19 September 2017
- 15:5115:51, 19 September 2017 diff hist −3 ECFP4 Best First Clustering No edit summary current
- 15:5015:50, 19 September 2017 diff hist +226 ECFP4 Best First Clustering No edit summary
- 05:4705:47, 19 September 2017 diff hist 0 DOCK 3.7 →Post Docking Clustering
- 05:4405:44, 19 September 2017 diff hist +511 Large-scale TC Calculations No edit summary current
- 05:3505:35, 19 September 2017 diff hist +509 ECFP4 Best First Clustering No edit summary
- 01:3401:34, 19 September 2017 diff hist −1 Large-scale SMILES Requesting and Fingerprints Converting No edit summary current
- 00:1300:13, 19 September 2017 diff hist +16 Large-scale SMILES Requesting and Fingerprints Converting No edit summary
- 00:0800:08, 19 September 2017 diff hist 0 Large-scale SMILES Requesting and Fingerprints Converting No edit summary
18 September 2017
- 23:5423:54, 18 September 2017 diff hist +1 Bemis-Murcko Scaffold Analysis No edit summary
- 23:5423:54, 18 September 2017 diff hist +43 Bemis-Murcko Scaffold Analysis No edit summary
- 23:5123:51, 18 September 2017 diff hist +1 Bemis-Murcko Scaffold Analysis No edit summary
- 23:5123:51, 18 September 2017 diff hist +555 Bemis-Murcko Scaffold Analysis No edit summary
- 23:4623:46, 18 September 2017 diff hist +26 Large-scale SMILES Requesting and Fingerprints Converting No edit summary
- 23:3923:39, 18 September 2017 diff hist +666 Bemis-Murcko Scaffold Analysis No edit summary
- 23:3523:35, 18 September 2017 diff hist +871 Bemis-Murcko Scaffold Analysis No edit summary
- 23:2723:27, 18 September 2017 diff hist +186 Large-scale TC Calculations No edit summary
- 23:2023:20, 18 September 2017 diff hist +762 Large-scale TC Calculations No edit summary
- 23:0923:09, 18 September 2017 diff hist +190 N Large-scale TC Calculations Created page with "Written by Jiankun Lyu, 20170918 Please run Large-scale SMILES Requesting and Fingerprints Converting first to get the SMILES and fingerprints files, then run the TC calc..."
- 23:0523:05, 18 September 2017 diff hist −36 DOCK 3.7 No edit summary
- 23:0523:05, 18 September 2017 diff hist +2,874 N Large-scale SMILES Requesting and Fingerprints Converting Created page with "Written by Jiankun Lyu, 20170918 The hierarchy of the directories: smiles_requesting/----- working/ | | | |----..."
- 23:0423:04, 18 September 2017 diff hist 0 DOCK 3.7 No edit summary
- 23:0323:03, 18 September 2017 diff hist +64 DOCK 3.7 No edit summary
- 23:0123:01, 18 September 2017 diff hist +563 Large-scale SMILES requesting No edit summary current
- 22:4422:44, 18 September 2017 diff hist +190 Large-scale SMILES requesting No edit summary
- 22:3922:39, 18 September 2017 diff hist +152 Large-scale SMILES requesting No edit summary
- 22:3322:33, 18 September 2017 diff hist +186 Large-scale SMILES requesting No edit summary
- 22:2522:25, 18 September 2017 diff hist +612 Large-scale SMILES requesting No edit summary
- 22:1922:19, 18 September 2017 diff hist +115 Large-scale SMILES requesting No edit summary
- 22:1822:18, 18 September 2017 diff hist +880 Large-scale SMILES requesting No edit summary
- 21:5921:59, 18 September 2017 diff hist +20 Large-scale SMILES requesting No edit summary
- 21:5821:58, 18 September 2017 diff hist +156 N Large-scale SMILES requesting Created page with "Written by Jiankun Lyu, 20170918 This tutorial is for requesting a large number of SMILES from ZINC server. Usually, the number is larger than 5M ZINC IDs."
- 21:5421:54, 18 September 2017 diff hist +36 DOCK 3.7 →Post Docking Clustering
- 21:5321:53, 18 September 2017 diff hist +59 N Bemis-Murcko Scaffold Analysis Created page with "= Getting SMILES for ZINC compounds you are interested in ="
- 21:4821:48, 18 September 2017 diff hist +96 DOCK 3.7 No edit summary
13 September 2017
- 20:4120:41, 13 September 2017 diff hist +161 ECFP4 Best First Clustering No edit summary
- 20:3020:30, 13 September 2017 diff hist +435 N ECFP4 Best First Clustering Created page with "Run the script at where your extract_all.sort.uniq.txt locates cd where your extract_all.sort.uniq.txt locates csh ~jklyu/zzz.script/large_scale_docking/cluster_analysis/be..."
- 20:2620:26, 13 September 2017 diff hist +62 DOCK 3.7 No edit summary
- 19:1419:14, 13 September 2017 diff hist +169 Substructure searching No edit summary current
- 19:0119:01, 13 September 2017 diff hist −583 Substructure searching No edit summary
- 18:5818:58, 13 September 2017 diff hist +4 Substructure searching No edit summary
- 18:2618:26, 13 September 2017 diff hist +247 Substructure searching No edit summary
- 18:2118:21, 13 September 2017 diff hist +499 Substructure searching No edit summary
- 18:1218:12, 13 September 2017 diff hist 0 File:Subsearching fig2.png Jklyu uploaded a new version of "File:Subsearching fig2.png" current
- 18:0518:05, 13 September 2017 diff hist 0 N File:Subsearching fig2.png No edit summary
- 18:0518:05, 13 September 2017 diff hist +78 Substructure searching No edit summary
- 18:0318:03, 13 September 2017 diff hist 0 N File:Subsearching fig1.png No edit summary current
- 18:0218:02, 13 September 2017 diff hist +102 Substructure searching No edit summary
- 18:0018:00, 13 September 2017 diff hist +731 Substructure searching No edit summary
- 17:4417:44, 13 September 2017 diff hist −21 Substructure searching No edit summary
- 17:3917:39, 13 September 2017 diff hist +1,049 N Substructure searching Created page with "Written by Jiankun Lyu, 2017/09/13 The hierarchy of the directories: thin_spheres_parameter_scanning----- working ..."
- 17:3417:34, 13 September 2017 diff hist +52 DOCK 3.7 No edit summary
5 May 2017
- 17:1017:10, 5 May 2017 diff hist +211 Tutorial on running Molecular Dynamics for GIST grid generation with scripts →Run MD
4 May 2017
- 00:0200:02, 4 May 2017 diff hist +141 Tutorial on running Molecular Dynamics for GIST grid generation with scripts →Run MD
3 May 2017
- 23:5723:57, 3 May 2017 diff hist +79 Tutorial on running Molecular Dynamics for GIST grid generation with scripts →Run MD
3 February 2017
- 22:0822:08, 3 February 2017 diff hist −6 How to do parameter scanning No edit summary
- 22:0622:06, 3 February 2017 diff hist −6 How to do parameter scanning No edit summary
19 January 2017
- 07:3907:39, 19 January 2017 diff hist +900 How to do parameter scanning No edit summary
- 07:2807:28, 19 January 2017 diff hist +60 How to do parameter scanning No edit summary
- 07:2607:26, 19 January 2017 diff hist +892 How to do parameter scanning No edit summary
- 07:1207:12, 19 January 2017 diff hist +1,029 N How to do parameter scanning Created page with "Written by Jiankun Lyu, 2017/01/18 The hierarchy of the directory: thin_spheres_parameter_scanning----- std_dockprep ------ dockfiles | ..."
20 September 2016
- 16:2816:28, 20 September 2016 diff hist +167 DOCK 3.7 tart No edit summary
18 September 2016
- 00:2000:20, 18 September 2016 diff hist +7,230 N DOCK 3.7 2016/09/16 Tutorial for Enrichment Calculations (Trent & Jiankun) Created page with "This tutorial uses the DOCK-3.7-beta3. This is a supplemental tutorial for DOCK 3.7 2015/04/15 abl1 Tutorial. Former one works well and is very simple and clear. This tutorial..."
- 00:2000:20, 18 September 2016 diff hist +32 DOCK 3.7 No edit summary
- 00:1600:16, 18 September 2016 diff hist −190 DOCK 3.7 2016/09/16 abl1 Tutorial(building) No edit summary current
17 September 2016
- 23:4123:41, 17 September 2016 diff hist +1,662 DOCK 3.7 2016/09/16 abl1 Tutorial(building) No edit summary
- 23:2623:26, 17 September 2016 diff hist +664 DOCK 3.7 2016/09/16 abl1 Tutorial(building) No edit summary
- 23:1023:10, 17 September 2016 diff hist +3,915 DOCK 3.7 2016/09/16 abl1 Tutorial(building) No edit summary
- 23:0123:01, 17 September 2016 diff hist +453 DOCK 3.7 2016/09/16 abl1 Tutorial(building) No edit summary
- 22:3822:38, 17 September 2016 diff hist +53 DOCK 3.7 2016/09/16 abl1 Tutorial(building) No edit summary
- 19:2019:20, 17 September 2016 diff hist +292 DOCK 3.7 2016/09/16 abl1 Tutorial(building) No edit summary
- 19:0519:05, 17 September 2016 diff hist +4 DOCK 3.7 2016/09/16 abl1 Tutorial(building) No edit summary
- 00:0800:08, 17 September 2016 diff hist +2 DOCK 3.7 2016/09/16 abl1 Tutorial(building) No edit summary
- 00:0600:06, 17 September 2016 diff hist +375 N DOCK 3.7 2016/09/16 abl1 Tutorial(building) Created page with "This tutorial uses the DOCK-3.7-beta3. This is for a Linux environment and the scripts assume that you are running on SGE queueing system. == set up directories == Go to th..."
16 September 2016
- 23:5823:58, 16 September 2016 diff hist +10 DOCK 3.7 No edit summary
- 23:5623:56, 16 September 2016 diff hist +476 N DOCK 3.7 2016/09/16 abl1 Tutorial Created page with "This tutorial uses the DOCK-3.7-beta3. This is for a Linux environment and the scripts assume that you are running on SGE queueing system. == Set up directories == Create d..." current
- 23:1823:18, 16 September 2016 diff hist +14 DOCK 3.7 No edit summary
- 23:1623:16, 16 September 2016 diff hist +1 m DOCK 3.7 2015/04/15 abl1 Tutorial No edit summary
- 22:1822:18, 16 September 2016 diff hist +26 DOCK 3.7 →Start here