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subsets [2016/12/27 22:07]
rkiss
subsets [2016/12/27 22:23]
rkiss
Line 28: Line 28:
 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. 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 exclusionto 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 elminiationThen, 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.
subsets.txt · Last modified: 2016/12/27 22:23 by rkiss