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subsets [2016/12/27 20:58] rkisssubsets [2016/12/27 21:19] 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. 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 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.
  
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subsets.txt · Last modified: 2016/12/27 21:23 by rkiss