This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision | ||
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 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. |