similaritysearch
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similaritysearch [2012/10/11 22:13] – created rkiss | similaritysearch [2012/10/15 07:47] – rkiss | ||
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====== Similarity search ====== | ====== Similarity search ====== | ||
+ | {{: | ||
Similarity search is for finding structurally similar molecules to a query molecule. | Similarity search is for finding structurally similar molecules to a query molecule. | ||
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- | Similarity search can be particularly useful for finding close analogs for a reference ligand or an initial hit identified by biological screening (e.g. HTS (link)). Close analogs of actives are expected to show some activity (similarity paradigm) and they can be used to build an initial SAR (structure-activity relationship) around a scaffold. | + | Similarity search can be particularly useful for finding close analogs for a reference ligand or an initial hit identified by biological screening (e.g. [[http:// |
===== How to use ===== | ===== How to use ===== | ||
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- | Descriptor | + | == Descriptor |
- | Mathematical representation of molecules used in the similarity/ | + | |
- | Similarity metric | + | Mathematical representation of molecules used in the similarity/ |
- | Tanimoto coefficient (http:// | + | |
+ | == Similarity metric | ||
+ | |||
+ | [[http:// | ||
+ | |||
+ | == Similarity threshold == | ||
- | Similarity threshold | ||
The similarity threshold is the minimum similarity value between the query and target molecules (set to 0.6 by default). A similarity value of 1 means that the two molecules cannot be distinguished by the selected descriptor and similarity metric. If the similarity search does not yield any hits with the default threshold, it makes sense to set a lower threshold and try again. | The similarity threshold is the minimum similarity value between the query and target molecules (set to 0.6 by default). A similarity value of 1 means that the two molecules cannot be distinguished by the selected descriptor and similarity metric. If the similarity search does not yield any hits with the default threshold, it makes sense to set a lower threshold and try again. | ||
- | Queries can be drawn by the molecule sketcher | + | Queries can be drawn by the [[sketcher|molecule sketcher]], which can be hidden and reopened by clicking on the “Hide/ |
===== Results ===== | ===== Results ===== | ||
- | - molecules | + | * Molecules |
- | - Tanimoto coefficient showing the similarity between the query and the target molecules will be displayed as a single column in Table (link) | + | |
- | - hits will be ordered by similarity score | + | * Hits will be ordered by similarity score |
similaritysearch.txt · Last modified: 2013/02/27 14:30 by rkiss