User contributions for Jklyu

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