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--- 1clickscaffoldhop [2013/12/02 23:39] – smaller screenshot sanmark
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-====== 1-CLICK SCAFFOLD HOP ======
-=== Identify completely new active scaffolds and leads with a single click! ===
-**[[http://www.youtube.com/watch?v=_T2Vx-LM6Bw|WATCH TUTORIAL VIDEO!]]**
-{{:1click_sh.png?600|}}
-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.
-====== When to use ======
-Hit identification: find novel actives by using a single reference ligand (ligand-based virtual screening)
-Lead optimization: replace parts of lead molecules to fix IP, toxicity, selectivity, pharmacokinetic issues
-====== How to use ======
-Draw a known active ligand and jump to a new active scaffold by clicking on Scaffold Hop! To understand why the two molecules are similar click on “Visualize similarity” when browsing the results. To purchase any of the hits click on the orange **"Quote"** buttons. **[[http://www.youtube.com/watch?v=_T2Vx-LM6Bw|Click here]]** for a tutorial video.
-====== Results ======
-{{:1click_sh_results2.png?600|}}
-====== Protocol ======
-=== FTrees ===
-[[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 ===
-[[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:
-== Input: ==
-[[purchasable|Purchasable compounds collection]]
-== 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]]
-  - [[sampler|Sampler]]
-      * Output: 500,000 compounds (randomized)
-  - [[diversitysel|Diversity selection]]
-      * Similarity threshold: 1.0
-      * Max number of most diverse molecules: 10,000