BoBER: Usage example

  1. Input drug structure
  2. Clicking the Example structure button will input the structure (a MurF inhibitor) in the molecular editor. The submit query button will execute the fragmenting procedure and and a new window will be displayed.

    Input drug structure

  3. Fragment selection
  4. We click on the fragment (tetrahydro-benzothiophene) we wish to replace within the query structure. We select the Intra-Family radio button within the Custom options and as the structure is quite unique, we also select the Interchangable join atoms radio button to expande the chemical space from which the bioisosteric replacements are sought. All other options are left as they are. Clicking the Submit query button will open the Results window.

    Fragment selection

  5. Results
  6. We can observe that BoBER found, in this case, one bioisosteric replacement for our fragment (tetrahydrohydro-thienopyridine). The same colored join atoms (red) and N.sp2 are the ones to overlap within the BoBER database. Clicking the glyphicon icon shows a dropdown menu of overlaping join atoms (in this case only one pair) at which the replacement should take place.


    Selecting the join pair opens the molecular editor where the structure with the bioisosteric replacement is shown:

Only one join atom pair can be selected. Other connections will be formed based on proximity of atoms and their valances.