diversity_selection
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
diversity_selection [2012/07/03 11:50] – [Limitations] sanmark | diversity_selection [2013/10/11 12:29] (current) – removed rkiss | ||
---|---|---|---|
Line 1: | Line 1: | ||
- | ====== Diversity selection ====== | ||
- | |||
- | This filter selects the most diverse compounds from large compound collections by eliminating of the most similar structures. The size of the input collection is decreased, while the maximum possible coverage of its represented chemical space is retained. | ||
- | |||
- | ===== 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. Collecting compounds from different regions of the chemical space is an efficient strategy to maximize the diversity of the identified active scaffolds. | ||
- | |||
- | 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 ===== | ||
- | |||
- | It is recommended to apply structural or phys-chem property filters prior to diversity selection to eliminate unwanted structures. This is important to avoid exotic structures that are typically identified as very diverse by the algorithm. | ||
- | ==== Basic options ==== | ||
- | |||
- | The following options can be used to control the diversity of the resulting collection. | ||
- | |||
- | * **Similarity threshold**: | ||
- | * **Number of most diverse molecules**: | ||
- | |||
- | If you do not limit the selection, the full collection will be returned ordered by diversity. This means that the top N molecules in the resulting collection will be the most diverse N molecules. The //maximum similarity// | ||
- | |||
- | ==== Advanced options ==== | ||
- | |||
- | Under Advanced options, you can adjust the definition of similarity/ | ||
- | |||
- | You will be able to set different similarity metrics as the measure of similarity. Currently, only the Tanimoto coefficient (Jaccard index)((http:// | ||
- | |||
- | We plan to introduce more descriptors and more similarity measure types in the future. | ||
- | |||
- | * **Molecular descriptor**: | ||
- | |||
- | ==== Default options ==== | ||
- | |||
- | The default descriptor used is the linear fingerprint implemented in OpenBabel ((Open Babel v2.3.90 http:// | ||
- | ==== 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: | ||
- | |||
- | - Calculate the similarity matrix of the molecules in the input collection | ||
- | - Process the matrix elements as follows: | ||
- | - Select the largest off-diagonal element in the similarity matrix | ||
- | - Eliminate one molecule of the most similar molecule pair randomly | ||
- | - 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 | ||
- | |||
- | During this process, the size of the collection is reduced while the diversity of the collection is increased. Each elimination step filters out one molecule that has close analogues in the remaining set. As a result, the remaining molecules will have a decreased similarity (increased diversity). | ||
- | |||
- | 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 ===== | ||
- | |||
- | Diversity selection filter is freely accessible for registered mcule users. Monthly limit is set to 10,000 input molecules. Your usage limits including the number of remaining molecules can be tracked under user profile / limits. To check your user profile click on your user name in the upper right corner on the mcule.com website. If you would like to run the Diversity selection filter for larger collections, | ||
- | |||
- | The average run time for 10,000 input molecules about a minute. | ||
- | |||
- | |||
- | ===== Changelog ===== | ||
- | |||
- | --- | ||
diversity_selection.1341316201.txt.gz · Last modified: 2012/07/03 11:50 by sanmark