diversity_selection
Differences
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diversity_selection [2012/06/28 13:17] – [Limitations] sanmark | diversity_selection [2012/07/03 11:50] – [Limitations] sanmark | ||
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====== Diversity selection ====== | ====== Diversity selection ====== | ||
- | This filter selects the most diverse compounds from large compound collections | + | This filter selects the most diverse compounds from large compound collections |
===== When to use ===== | ===== When to use ===== | ||
- | If you have limited experimental or computational resources, diversity selection is an unbiased way to limit the number of compounds to handle. | + | If you have limited experimental or computational resources, diversity selection is an unbiased way to limit the number of compounds to handle. |
- | + | ||
- | Using this filter you can select a diverse, representative set of your virtual hits, or effectively reduce your screening/ | + | |
+ | Using this filter you can either reduce the size of large (virtual) screening libraries, or select a diverse, representative set of your virtual hits. | ||
===== How to use ===== | ===== How to use ===== | ||
- | It is recommended | + | It is recommended |
==== Basic options ==== | ==== Basic options ==== | ||
Line 20: | Line 18: | ||
* **Number of most diverse molecules**: | * **Number of most diverse molecules**: | ||
- | If you don’t | + | If you do not limit the selection, the full collection will be returned |
==== Advanced options ==== | ==== Advanced options ==== | ||
- | You can adjust the meaning | + | Under Advanced options, you can adjust the definition |
- | * **Molecular descriptor**: | + | You will be able to set different similarity metrics as the measure of similarity. Currently, only the Tanimoto coefficient (Jaccard index)((http:// |
- | ==== Default options ==== | + | We plan to introduce more descriptors and more similarity measure types in the future. |
- | The default | + | * **Molecular |
- | If you have no suggestions to use another setup, you can rely on our choices. After implementation and evaluation of new fingerprints and metrics, the default setup can be changed. This can be tracked at the end of this document, in the Changelog section. | + | ==== Default options ==== |
+ | The default descriptor used is the linear fingerprint implemented in OpenBabel ((Open Babel v2.3.90 http:// | ||
==== Algorithm ==== | ==== Algorithm ==== | ||
- | We use an optimized implementation of the stepwise elimination algorithm((R. J. Taylor, J. Chem. Inf. Comput. Sci., 1995, 35, 59 67.)), which can be described as follows: | + | We use an optimized implementation of the stepwise elimination algorithm((R. J. Taylor, J. Chem. Inf. Comput. Sci., 1995, 35, 59-67.)), which can be described as follows: |
- | - calculate | + | - Calculate |
- | - process | + | - Process |
- | - select | + | - Select |
- | - eliminate | + | - Eliminate |
- | - go to step I. if off-diagonal elements remained | + | - Go to step I. if off-diagonal elements remained |
- | - sort the list of eliminated molecules by similarity values associated to the elimination steps in increasing order | + | - Sort the list of eliminated molecules by similarity values associated to the elimination steps in increasing order |
- | During this process, the size of the collection is reduced | + | During this process, the size of the collection is reduced |
- | + | ||
- | After the algorithm finishes, structures are sorted by similarity | + | |
+ | After the algorithm finishes, structures are sorted by similarity values and are placed in the result collection. The first molecules in the resulted collection are the most dissimilar (most diverse) ones. The length of the result list is determined by input parameters: maximum number of compounds and similarity threshold. | ||
===== Limitations ===== | ===== Limitations ===== | ||
- | The diversity | + | Diversity |
+ | |||
+ | The average run time for 10,000 input molecules about a minute. | ||
===== Changelog ===== | ===== Changelog ===== |