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--- subsets [2016/12/27 22:07]
rkiss
+++ subsets [2016/12/27 22:23]
rkiss
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 The [[https://mcule.com/database/|downloadable files]] contain the compounds in diversity order i.e. the first N compounds represent the most dissimilar N compounds. This means that if you want to further narrow down the number of compounds you can keep the first X compounds of the files and they will be the most dissimilar ones.
-Structural similarity was measured by Tanimoto coefficient (TC) between FP2 linear fingerprints generated by [[http://jcheminf.springeropen.com/articles/10.1186/1758-2946-3-33|OpenBabel]]. The combinations of the following algorithms were applied to extract the most dissimilar subsets:
+Structural similarity was measured by Tanimoto coefficient (TC) between FP2 linear fingerprints generated by [[http://jcheminf.springeropen.com/articles/10.1186/1758-2946-3-33|OpenBabel]]. The combinations of the following algorithms were applied to extract the most dissimilar compounds:
-  * we used sphere exclusion to eliminate highly similar compounds to reduce the input size where needed
+  * sphere exclusion: to quickly eliminate highly similar compounds to reduce the input collection to a manageable size for the subsequent [[diversitysel|stepwise elimination]] algorithm
-  * then [[diversitysel|stepwise elimination]] was applied to obtain the most dissimilar compounds
+  * [[diversitysel|stepwise elimination]]: a more thorough algorithm that eliminates one molecule of the most similar molecule pairs
-In sphere exclusion we used the stock compounds first as "centers" for the elimination of redundant compounds, and we retained the stock compounds during the stepwise elimination.
+In sphere exclusion we used the in-stock compounds first as "centers" and eliminated their most similar analogs, while during [[diversitysel|stepwise elimination]] we retained the in-stock compounds from the most similar molecule pairs.
-===== Subsets =====
-To speed up the selection, we used sphere exclusion in case of the Ro5 subsets with TC=0.8 to pass at most 3M compounds for stepwise elminiation. Then, the following subsets were saved:
-^Subset name			^Input	^Property filter	^Diversity	^Subset size ^
-|Mcule Purchasable (In Stock Ro5 Diverse 1M) |Stock compounds|rule-of-5, max 1 violation|top diverse 1M, max TC: 0.8|1,000,000|
-|Mcule Purchasable (In Stock Ro5 Diverse 350K)|Stock compounds|rule-of-5 (max 1 violation)|Top diverse 350K, max TC:0.7|350,000|
-|Mcule Purchasable (In Stock Ro3)|Stock compounds|rule-of-3 (max 1 violation)|-|154,238|
-|Mcule Purchasable (In Stock Ro3 Diverse 50K)|Stock compounds|rule-of-3 (max 1 violation)|Top diverse 50K, max TC: 0.8|50,000|
-|Mcule Purchasable (In Stock & Virtual Ro3)|Stock compounds + virtual compounds|rule-of-3 (max 1 violation)|-|789,907|
-|Mcule Purchasable (In Stock & Virtual Ro3 Diverse 70K)|Stock compounds + virtual compounds|rule-of-3 (max 1 violation)|Top diverse 70K, max TC: 0.8|70,000|
+Sphere exclusion diversity selection was applied in case of the rule-of-5 subsets with maximum TC=0.8 and a maximum of 3M compounds that were subjected to stepwise elimination.

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