September Design a Molecule

Detailed steps on how to enter the design competiton are presented below. Or watch the video version.

  1. Enter the competition to get everything you need
  2. Download the zip file using the link in the email that you get sent
  3. Unzip the downloaded file and follow the instructions in the readme document
  4. Install FieldAlign and FieldView from the “Software” folder
  5. In the “Competition” folder Double click the left mouse button on the FieldAlign project: “START_HERE_Sep11.fpj” to open this file in FieldAlign.
  6. Note two 2d molecules present in the molecule table: the reference (yellow block background) and four disconnected fragments (query)
  7. Select the query molecule in the table with the left mouse button (should turn to a blue background).
  8. Right click and select “Edit a copy of the selected molecule” to open the Molecule editor.
  9. Hold LMB on background and move mouse to rotate view.
  10. Edit (add atom) by dragging and holding LMB from a fragment. Ctrl-Z will undo. Hold Ctrl will toggle selection mode. Delete will delete selected atoms.
  11. Repeat to connect the fragments and design the replacement core using whichever atoms you wish: Select from the left hand atom menu; double click on a bond to toggle bonding.
  12. Minimise core only: Using the selection tool highlight the core (cyan) click minimise.
  13. Once you are happy: Save to exit the editor.
  14. To align the new molecule query and calculate a similarlty score: Click process (calculate icon) in the top menu.
  15. Repeat the process to refine the design or start again from the fragments.
  16. Once you have a winning design, export the molecule: Select the molecule to export by left clicking on it in the table then use File menu -> Export -> Export selected molecule
  17. Save the molecule to an sdf file
  18. Upload the molecule to enter or send it to

Try Cresset solutions on your project

Request a free software evaluation