Molecule Search Page

The Molecule Search page provides the ability to search using similarity in two or three dimensions; with substructures; using matches with search terms; and by molecule title.

The searches are comparable to the searches performed previously by OpenEye’s MaaS and FastROCS web services. Searches can be launched from a number of places in the Orion user interface, and results can be stored in files or datasets for use in other Orion operations.


Figure 1. Molecule Search

You can search with a variety of criteria.

For a demonstration of the 2D feature, see the following video.

Search by Sketch

You can sketch a molecule with such tools as Fragment (fragment_icon), Templates (template_icon), and Atoms (atom_icon). You can also send a molecule from other pages such as Analyze, by selecting the molecule, right clicking, and choosing Send to Search. Then select a database from the list on the right side of the screen, such as Enamine Simple, and enter search parameters (in this example, the fingerprint type, Tanimoto score, and maximum number of hits).


Figure 2. 100 Matches for a query.

You can use any of the search results as input for a new search. Click on a molecule in the search results to select it, then click on its kebab menu (kebab_icon), and select New Search. Alternatively, you can copy the found molecule as a title, SMILES string, or MOL file.


Figure 3. Use a search result for further work.


Figure 4. 3D results from a preceding 2D search result.

Notice that a toggle allows you to choose 2D or 3D representations of the search results, after a 3D similarity search.

Save Results

You can save the search results to a dataset or file, or you can send the results directly to the Analyze page.


Figure 5. Retaining the results of a search.

Search History

Orion retains the history of your searches automatically. They are cleared after 30 days unless you pin them.


Figure 6. Pin queries to save them indefinitely.

Search by Title

A title search will populate the Sketcher with any structure in the selected database that matches the name.


Figure 7. Result of a search for the title “Aspirin.”