User Tools

Site Tools


This is an old revision of the document!

Preselected subsets of the Mcule database

We provide you with Ro5 and Ro3 subsets that can serve as a starting point of your virtual screening projects if you don't want to screen the full Mcule database (36M compounds currently). Structurally diverse subsets of the drug like and fragment like parts were generated to represent the same chemical space with a smaller number of compounds.


The subsets can be


Property based filtering

For the drug like and fragment like subsets the rule of 5 and rule of 3 rules were applied, allowing one violation. Additionally, we used a few more rules:

  • number of components < = 1
  • MW > = 100
  • number of N+O atoms > = 1
  • number of rings > = 1
  • number of halogens < = 7
  • number of inorganic atoms = 0

We used these rules to leave out more “strange compounds” which may be included more likely in the diverse sets as they differ from the regular compounds.

Diversity selection

The Mcule database contains ~5.7M stock compounds and ~30.3M virtual compounds. Diversity selection was carried out in a way to prefer the stock compounds over the virtual ones. As a result, the chemical space is represented by stock compounds where possible. More over, the downloadable files contains the compounds in diversity order i.e. the first N compounds represent the most dissimilar N compounds, so you can choose yourself the number of compounds to represent the whole Ro3 and Ro5 subsets.

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:

  • we used sphere exclusion to eliminate highly similar compounds to reduce the input size where needed
  • then stepwise elimination was applied to obtain the most dissimilar compounds

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.


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 compoundsrule-of-5, max 1 violationtop diverse 1M, max TC: 0.81,000,000
Mcule Purchasable (In Stock Ro5 Diverse 350K)Stock compoundsrule-of-5 (max 1 violation)Top diverse 350K, max TC:0.7350,000
Mcule Purchasable (In Stock Ro3)Stock compoundsrule-of-3 (max 1 violation)-154,238
Mcule Purchasable (In Stock Ro3 Diverse 50K)Stock compoundsrule-of-3 (max 1 violation)Top diverse 50K, max TC: 0.850,000
Mcule Purchasable (In Stock & Virtual Ro3)Stock compounds + virtual compoundsrule-of-3 (max 1 violation)-789,907
Mcule Purchasable (In Stock & Virtual Ro3 Diverse 70K)Stock compounds + virtual compoundsrule-of-3 (max 1 violation)Top diverse 70K, max TC: 0.870,000
subsets.1482436944.txt.gz · Last modified: 2016/12/22 21:02 by sanmark