diversitysel
Differences
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diversitysel [2012/10/13 17:49] – [Results] sanmark | diversitysel [2016/12/27 21:16] (current) – [Algorithm] rkiss | ||
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====== Diversity selection ====== | ====== Diversity selection ====== | ||
+ | {{: | ||
This filter selects the most diverse (dissimilar) molecules from collections by eliminating the closest analogs. Diversity selection reduces the size of the input collection and maximizes the coverage of the chemical space at the same time. | This filter selects the most diverse (dissimilar) molecules from collections by eliminating the closest analogs. Diversity selection reduces the size of the input collection and maximizes the coverage of the chemical space at the same time. | ||
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- | Exotic (non-druglike) molecules typically show large structural diversity. Consequently, | + | Exotic (non-druglike) molecules typically show large structural diversity. Consequently, |
==== Basic options ==== | ==== Basic options ==== | ||
- | Similarity threshold | + | == Similarity threshold |
- | No molecule pairs in the output collection can be more similar to each other than this number (Tanimoto coefficient). | + | |
+ | No molecule pairs in the output collection can be more similar to each other than this number ([[http:// | ||
+ | |||
+ | == Max number of most diverse molecules == | ||
- | Max number of most diverse molecules | ||
The diversity selection algorithm will output this number of molecules or less (if the “Similarity threshold” is reached first). | The diversity selection algorithm will output this number of molecules or less (if the “Similarity threshold” is reached first). | ||
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- | Descriptor | + | == Descriptor |
- | Mathematical representation of molecules used in the similarity/ | + | |
- | Tanimoto coefficient | + | Mathematical representation of molecules used in the similarity/ |
+ | |||
+ | [[http:// | ||
===== Results ===== | ===== Results ===== | ||
* diverse subset of the input collection satisfying the filter criteria | * diverse subset of the input collection satisfying the filter criteria | ||
- | * maximum similarity (found between any molecule pairs if the rank list is cut exactly after this molecule) will be displayed as a single column in Table (link) | + | * maximum similarity (found between any molecule pairs if the rank list is cut exactly after this molecule) will be displayed as a single column in Table and List views |
* output molecules will be ordered by maximum similarity (most diverse molecules are ranked highest) | * output molecules will be ordered by maximum similarity (most diverse molecules are ranked highest) | ||
===== Limits ===== | ===== Limits ===== | ||
- | Diversity selection available in the Free package | + | Diversity selection available in the [[freepackage|Free package]] is limited to 10,000 input molecules per month. To get access to unlimited Diversity selection, |
===== Algorithm ===== | ===== Algorithm ===== | ||
- | Diversity selection utilizes an optimized implementation of the stepwise elimination algorithm(ref4), which can be described as follows: | + | Diversity selection utilizes 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 | + | * 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 | + | - Eliminates |
- | 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). | + | |
- | The average run time for 10,000 input molecules | + | During this process, the size of the collection |
- | 1) http:// | ||
- | 2) Open Babel v2.3.90 http:// | ||
- | 4) R. J. Taylor, J. Chem. Inf. Comput. Sci., 1995, 35, 59-67. |
diversitysel.1350150542.txt.gz · Last modified: 2012/10/13 17:49 by sanmark