Do you ever…

…see molecules in your SYNTHIA™ results that you would not want to use in the lab?

Whether because of safety reasons, regulations, or personal preference, there may be certain compounds that you would generally avoid using in the lab. You can tell SYNTHIA™ to keep these molecules out of your search results by making a custom Molecule List. To view, create and manage these lists, open the dropdown menu for Predefined Lists of Molecules in either the Exclude or Seek section of the Analysis Configuration page.

You can click on any of the preloaded molecule lists to see which compounds are listed there or click on the New Molecule List button to start your own custom list.

Add molecules to a custom molecule list by drawing structures in the molecule editor, uploading a sdf or mol file, or searching for compounds by name in our databases of commercial and published compounds.

You can also copy or move molecules from existing molecule lists.

When you are setting up an analysis, you can choose a molecule list from the Predefined lists of molecules menu in the Exclude & Seek section of the Analysis Configuration page.

Any pathways including molecules from the selected lists will be highly penalized by the scoring function and should not appear in your top 50 pathways.

Find another molecule you want to avoid?

Once you have created a custom molecule list, it is easy to add additional unwanted molecules anytime you see them in your results. Just click on the molecule to open the molecule card, click ‘Add to molecule set’ and select a molecule list from the menu.

For more information on creating and managing Molecule Lists you can search for ‘molecule lists’ in the User Guide or contact our team at

synthia.help@milliporesigma.com