Compound to Fragment Decomposition

What is the purpose of this workflow?

To illustrate to people wanting to run fragment simulations using their own datasets, whose datasets are composed of compounds, how they can convert those compounds into fragment simulation ready fragments. It will also detail or cite the compound decomposition algorithm options so users can select the relevantly decomposed fragments.

Who is this workflow useful for?

  • People with custom compound set
  • People who need to turn compounds into fragment sets

Current Workflow Requirements

  • Have a BMaps account.
  • Compounds are in sdf files. - Files can contain single or multiple compounds in a single file, but each file should be less than 64 Kb to avoid a bug that is currently being fixed.

Workflow:

  1. Get your compound dataset into sdf files - mind the note on sizes above.
  2. Go to https://boltzmannmaps.com/ and login to BMaps.
  3. Click the Main Menu button in the upper right hand corner, then click "Fragment Search" from the dropdown menu to open a new tab with the Fragment Search interface.
  4. In the Fragment Search interface select the Main Menu  in the upper right hand corner, then click "Fragment Sets".
  5. In the "Fragment Sets" panel on the left side of the screen, click the  button. This will create a new fragment set with the automatically created name "fragset-[numerical date]". This can be changed by pressing the button in the updated right hand panel.
  6. In the right hand panel, select the button to open the following embedded menu.
  7. Choose your sdf file with the "Choose File" button. Note if you click the "Choose File" button and hit cancel then no file will be chosen.
  8. Click the checkmark for "Decompose into fragments". and press the OK button.
  9. If there are no problems you will see the menu report the following messages. This will close and populate the fragment list when completed. You may close the Fragment Search interface and return using step 3.
    If there are problems you may instead see this message:

    If after following provided instructions on refreshing you do not see your fragments, then an error may have occurred and we recommend using the contact us page to determine the problem. The most common problems at this time have to do with sdf files with multiple compounds having formatting errors or files being larger than the current allowable limit.
  10. After successfully decomposing the compounds into fragments the import window will disappear and you will see your new fragments named as [Original Compound filename]-[compound#]-[frag#]-[decomposition methodology].
    The Decomposition Methodologies are as follows:
    1. Recap
    2. BRICS
    3. Ring/No Ring - Internal methodology splitting at rings.
  11. Now that you have your fragments you can scroll over them to see a pop-up of the 2D structure of the fragments. You can choose to keep all of the created fragments in the set or remove some using the Select, Select None, Remove checked frags. buttons. You can also export the fragments to sdf using the Export SDF button to download the fragments. You can also add the set to the Fragment Simulation cart for later submission using the Add set to Cart button.
    Note that the duplicates have been removed.

Congratulations! You have now created a fragment set from compounds!