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--- 1clickscaffoldhop [2013/03/05 21:08] – rkiss
+++ 1clickscaffoldhop [2024/04/09 08:32] (current) – removed rkiss
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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?800|}}
-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?800|}}
-====== Protocol ======
-=== 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.
-=== 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:
-. 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
-. REOS
-. Sampler: output 500,000 compounds randomized
-. Diversity selection
-  * Similarity threshold: 1.0
-  * Max number of most diverse molecules: 10,000