User contributions for Iamkaant

21 September 2023

• 06:4106:41, 21 September 2023 diff hist +318‎ Extended Search of Analogs via Bioisosteric Replacements ‎ disclaimer added current
• 06:1606:16, 21 September 2023 diff hist +3,045‎ N Extended Search of Analogs via Bioisosteric Replacements ‎ Created page with "=== Rationale === Our standard pipeline of searching for analogs (at least as I know it) consists of entering the SMILES of a molecule of interest into all flavors of SmallWorld and Arthor, available in the lab. This procedure has two drawbacks: # Limited diversity. SmallWorld's and Arthor's measure of distance between the analogs and the parent compound is graph edit distance.<ref>I am probably using slightly wrong terminology here, so be it. You can learn more about..."

20 July 2023

• 00:2000:20, 20 July 2023 diff hist +2‎ m Global Matching Sphere Optimization ‎No edit summary current
• 00:1900:19, 20 July 2023 diff hist +176‎ m Global Matching Sphere Optimization ‎No edit summary
• 00:1600:16, 20 July 2023 diff hist −22‎ m Global Matching Sphere Optimization ‎No edit summary

17 July 2023

• 16:0416:04, 17 July 2023 diff hist +2,957‎ Global Matching Sphere Optimization ‎ updated to describe the new version of Juggler

31 May 2023

• 21:3621:36, 31 May 2023 diff hist +6‎ m Membrane Modeling ‎No edit summary current
• 21:2721:27, 31 May 2023 diff hist +19‎ m Membrane Modeling ‎No edit summary

3 May 2023

• 20:3820:38, 3 May 2023 diff hist −116‎ Global Matching Sphere Optimization ‎No edit summary

2 May 2023

• 00:0200:02, 2 May 2023 diff hist +2‎ m Global Matching Sphere Optimization ‎No edit summary
• 00:0100:01, 2 May 2023 diff hist +1‎ Global Matching Sphere Optimization ‎No edit summary
• 00:0100:01, 2 May 2023 diff hist +3‎ Global Matching Sphere Optimization ‎No edit summary
• 00:0000:00, 2 May 2023 diff hist +539‎ Global Matching Sphere Optimization ‎No edit summary

1 May 2023

• 23:0123:01, 1 May 2023 diff hist +91‎ Global Matching Sphere Optimization ‎No edit summary
• 23:0123:01, 1 May 2023 diff hist +35‎ N File:Combined metrics plot from a GA run.png ‎No edit summary current
• 19:5219:52, 1 May 2023 diff hist +871‎ Global Matching Sphere Optimization ‎No edit summary

30 April 2023

• 07:0607:06, 30 April 2023 diff hist +291‎ Global Matching Sphere Optimization ‎No edit summary
• 07:0107:01, 30 April 2023 diff hist +100‎ Global Matching Sphere Optimization ‎No edit summary
• 06:5906:59, 30 April 2023 diff hist −2‎ Global Matching Sphere Optimization ‎No edit summary
• 06:5806:58, 30 April 2023 diff hist +1,938‎ N Global Matching Sphere Optimization ‎ Created page with "== Goal == To optimize your matching sphere (MS) setups getting more enrichment with fewer spheres. == Description == The program performs optimization of matching spheres using genetic algorithm. It selects spheres from two sets: * heavy atoms of xtal-lig * spheres prepared by SPHGEN program At each generation, N matching sphere sets are created, containing a maximum of M spheres each. Then retrospective docking is done for each set, and sets are ranked by the enrichme..."

10 January 2023

• 17:5917:59, 10 January 2023 diff hist −5‎ Membrane Modeling ‎No edit summary Tag: Manual revert
• 17:5917:59, 10 January 2023 diff hist +5‎ m Membrane Modeling ‎No edit summary
• 17:5817:58, 10 January 2023 diff hist −5‎ User:Iamkaant ‎No edit summary current Tag: Manual revert
• 17:5817:58, 10 January 2023 diff hist +5‎ User:Iamkaant ‎No edit summary

31 October 2022

• 22:5822:58, 31 October 2022 diff hist +122‎ m Membrane Modeling ‎ added the note to export $SCHRODINGER variable before running the script

11 October 2022

• 17:4317:43, 11 October 2022 diff hist +30‎ m Synthesia ‎ →‎How to create this tree? current

4 September 2022

• 21:2021:20, 4 September 2022 diff hist +75‎ m Membrane Modeling ‎No edit summary
• 21:1921:19, 4 September 2022 diff hist +1,198‎ Membrane Modeling ‎ added the manual for membrane positioning

11 August 2022

• 18:5718:57, 11 August 2022 diff hist +134‎ Synthesia ‎ added retrosynthesis route generation by IBM RXN

3 August 2022

• 21:1121:11, 3 August 2022 diff hist −1‎ m Synthesia ‎No edit summary
• 21:1021:10, 3 August 2022 diff hist +666‎ Synthesia ‎ added retrosynthesis route generation tools
• 20:4920:49, 3 August 2022 diff hist −2‎ m Synthesia ‎No edit summary
• 20:4820:48, 3 August 2022 diff hist +91‎ Synthesia ‎No edit summary
• 20:4620:46, 3 August 2022 diff hist +31‎ m Synthesia ‎No edit summary
• 20:4420:44, 3 August 2022 diff hist +5,443‎ N Synthesia ‎ Created page with "<blockquote>Synthesia is a command-line tool that uses an entire retrosynthetic route as a guide pathway to generate optimized structural analogues of a lead compound without..."

14 June 2022

• 02:5102:51, 14 June 2022 diff hist +944‎ Membrane Modeling ‎ added troubleshooting of MD runs

6 June 2022

• 21:1421:14, 6 June 2022 diff hist +726‎ N Conversion of .rxn files to reaction SMARTS ‎ Created page with "DataWarrior folks have implemented enumeration protocol in their soft. It is published in 10.1021/acs.jcim.1c01041 They store reactions in .rxn format, which is documented in..." current

26 April 2022

• 06:5306:53, 26 April 2022 diff hist +209‎ m Membrane Modeling ‎ changed Pymol script: Hs are not removed from lipids

21 April 2022

• 01:4201:42, 21 April 2022 diff hist +1,593‎ Membrane Modeling ‎ added protocol for MemProtMD
• 01:2701:27, 21 April 2022 diff hist +8,059‎ Membrane Modeling ‎ Added protocol for MD in Schrodinger
• 01:0401:04, 21 April 2022 diff hist +1,999‎ Membrane Modeling ‎No edit summary

28 March 2022

• 19:4019:40, 28 March 2022 diff hist +79‎ Andrii's notes on SynthI ‎ added Synthons generated from CSSB00020671770 current
• 19:3519:35, 28 March 2022 diff hist +67‎ N File:CSSB00020671770.png ‎ All synthons generated by SynthI from CSSB00020671770 current
• 19:3319:33, 28 March 2022 diff hist +8‎ m Andrii's notes on SynthI ‎No edit summary

24 March 2022

• 05:0005:00, 24 March 2022 diff hist +40‎ m Andrii's notes on SynthI ‎No edit summary

22 March 2022

• 02:5002:50, 22 March 2022 diff hist +62‎ m Andrii's notes on SynthI ‎No edit summary
• 02:4802:48, 22 March 2022 diff hist +1,761‎ Andrii's notes on SynthI ‎ Manual for enumeration using new code.

16 March 2022

• 23:5323:53, 16 March 2022 diff hist +144‎ Andrii's notes on SynthI ‎No edit summary

15 March 2022

• 21:5621:56, 15 March 2022 diff hist +8‎ m Andrii's notes on SynthI ‎No edit summary
• 21:5321:53, 15 March 2022 diff hist +133‎ m Andrii's notes on SynthI ‎No edit summary