1clickscaffoldhop
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1clickscaffoldhop [2013/03/05 21:13] – [Protocol] rkiss | 1clickscaffoldhop [2013/12/02 23:39] – smaller screenshot sanmark | ||
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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:// | **[[http:// | ||
- | {{: | + | {{: |
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:// | + | [[https:// |
====== When to use ====== | ====== When to use ====== | ||
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====== Results ====== | ====== Results ====== | ||
- | {{: | + | {{: |
====== Protocol ====== | ====== Protocol ====== | ||
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=== FTrees === | === FTrees === | ||
- | [[https:// | + | [[https:// |
+ | |||
+ | In [[https:// | ||
=== Database === | === Database === | ||
- | [[https:// | + | [[https:// |
- | ==Input== | + | == Input: == |
[[purchasable|Purchasable compounds collection]] | [[purchasable|Purchasable compounds collection]] | ||
- | ==Workflow== | + | == Workflow: == |
- | + | ||
- | 1. mcule properties | + | |
- | + | ||
- | * Components | + | |
- | + | ||
- | * Heavy atoms Min: 10 | + | |
- | + | ||
- | * RO5 violations | + | |
- | + | ||
- | * 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 | + | |
- | + | ||
- | * Similarity threshold: 1.0 | + | |
- | + | ||
- | * Max number of most diverse molecules: 10,000 | + | |
+ | - [[basicpropertyfilter|Basic property filter]] | ||
+ | * Components | ||
+ | * Heavy atoms Min: 10 | ||
+ | * RO5 violations | ||
+ | * 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 |