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1clickscaffoldhop [2013/03/05 21:08] rkiss1clickscaffoldhop [2014/02/26 00:01] (current) flack
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-====== 1-Click Scaffold Hop ======+====== 1-CLICK SCAFFOLD HOP ======
  
 === Identify completely new active scaffolds and leads with a single click! === === Identify completely new active scaffolds and leads with a single click! ===
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 **[[http://www.youtube.com/watch?v=_T2Vx-LM6Bw|WATCH TUTORIAL VIDEO!]]** **[[http://www.youtube.com/watch?v=_T2Vx-LM6Bw|WATCH TUTORIAL VIDEO!]]**
  
-{{:1click_sh.png?800|}}+{{:1click_sh.png?600|}}
  
 Scaffold hopping: identifying novel and diverse scaffolds starting from a single reference ligand Scaffold hopping: identifying novel and diverse scaffolds starting from a single reference ligand
-[[https://mcule.com/apps/1-click-scaffold-hop|1-Click Scaffold Hop]] is the simplest online solution for scaffold hopping.+[[https://mcule.com/apps/1-click-scaffold-hop/|1-Click Scaffold Hop]] is the simplest online solution for scaffold hopping.
  
 ====== When to use ====== ====== When to use ======
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 ====== Results ====== ====== Results ======
  
-{{:1click_sh_results2.png?800|}}+{{:1click_sh_results2.png?600|}}
  
 ====== Protocol ====== ====== Protocol ======
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 === FTrees === === FTrees ===
  
-[[https://mcule.com/apps/1-click-scaffold-hop|1-Click Scaffold Hop]] utilizes the [[http://www.biosolveit.de/FTrees|FTrees algorithm]]. FTrees is a highly efficient ligand-based tool particularly suitable for fuzzy similarity searching, scaffold hopping and virtual screening. FTrees represents molecules by a tree-like representation where pharmacophore properties are stored instead of atom-level structural information (Feature Tree). Feature Trees of two molecules are compared and an FTrees similarity score is calculated. Typically, an FTrees score above 0.85 corresponds to a meaningful similarity between the query and the hit molecules. The topological FTrees descriptor enables the visualization of the similarity by showing the similar substructures and their contribution to the overall similarity.+[[https://mcule.com/apps/1-click-scaffold-hop/|1-Click Scaffold Hop]] is powered by [[ftrees|FTrees Visual similarities]]. FTrees Visual Similarities is a highly efficient ligand-based tool particularly suitable for fuzzy similarity searching, scaffold hopping and virtual screening. The underlying [[http://www.biosolveit.de/FTrees|FTrees algorithm]] represents molecules by a tree-like representation where pharmacophore properties and topology of the molecules are stored while atomic-level structural information is ignored (Feature Tree). Feature Trees of two molecules are compared and an FTrees similarity score is calculated. Typically, an FTrees score above 0.85 corresponds to a meaningful similarity between the query and the hit molecules. The topological FTrees descriptor enables the visualization of the similarity by highlighting the similar substructures and their contribution to the overall similarity score. 
 + 
 +In [[https://mcule.com/apps/1-click-scaffold-hop/|1-Click Scaffold Hop]], [[ftrees|FTrees Visual Similarities]] is running with default parameters.
  
 === Database === === Database ===
  
-[[https://mcule.com/apps/1-click-scaffold-hop|1-Click Scaffold Hop]] runs an FTrees search for the input query molecule on a special subset of the mcule database. This subset has been prefiltered as follows: +[[https://mcule.com/apps/1-click-scaffold-hop/|1-Click Scaffold Hop]] is basically an FTrees search with the input query molecule on a special subset of the mcule database containing 10,000 diverse compounds. This subset has been generated as follows:
- +
-1. mcule properties +
- +
-  * Components   Max: 1 +
- +
-  * Heavy atoms   Min: 10 +
- +
-  * RO5 violations   Max: 0 +
- +
-  * Mass   Min: 200 +
- +
-  * Rotatable bonds   Max: 8 +
- +
-  * Rings   Min: 1 +
- +
-  * N/O atoms   Min: 1 +
- +
-2. REOS  +
- +
-3. Sampler: output 500,000 compounds randomized+
  
-4. Diversity selection+== Input: ==
  
-  * Similarity threshold: 1.0+[[purchasable|Purchasable compounds collection]]
  
-  * Max number of most diverse molecules10,000+== Workflow==
  
 +  - [[basicpropertyfilter|Basic property filter]]
 +      * Components   Max: 1
 +      * Heavy atoms   Min: 10
 +      * RO5 violations   Max: 0
 +      * Mass   Min: 200
 +      * Rotatable bonds   Max: 8
 +      * Rings   Min: 1
 +      * N/O atoms   Min: 1
 +  - [[reos|REOS]]
 +  - [[diversitysel|Diversity selection]]
 +      * Similarity threshold: 1.0
 +      * Max number of most diverse molecules: 10,000
1clickscaffoldhop.1362517719.txt.gz · Last modified: 2013/03/05 21:08 by rkiss