User contributions for Iamkaant

22:3922:39, 5 December 2025 diff hist +9,211‎ N Create ChemDraw files with Python ‎ Created page with "== Complete Manual: Displaying Chemical Structures in ChemDraw Format Using pycdxml == === Overview === The pycdxml package enables platform-independent manipulation of ChemDraw files (CDX and CDXML formats) through Python. The CDXMLSlideGenerator module creates professional structure sheets by arranging molecules in grids with associated properties, outputting standard ChemDraw documents that can be further edited by users. === Installation === Create a conda enviro..." current

22:2122:21, 31 October 2025 diff hist +5,549‎ N Juggler ‎ first draft current

22:3022:30, 6 October 2025 diff hist +4‎ m Interactive Molecular Structure Alignment App for QSAR ‎No edit summary current
22:2822:28, 6 October 2025 diff hist +131‎ m Interactive Molecular Structure Alignment App for QSAR ‎ added path to the program
21:0221:02, 6 October 2025 diff hist +10,264‎ N Interactive Molecular Structure Alignment App for QSAR ‎ Created page with "= Interactive Molecular Structure Alignment Application = A PyQt5-based interactive tool for aligning and visualizing molecular analogs with customizable highlighting, transformations, and high-resolution export capabilities. == Table of Contents == * Installation * Quick Start * Features * User Interface * Workflows * File Formats * #Troubleshooting|Troubleshooting..."

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..."

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

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..."

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

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

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

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..."

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

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

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

01:4201:42, 21 April 2022 diff hist +1,593‎ Membrane Modeling ‎ added protocol for MemProtMD

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