Create, import, and search for molecule entities

Molecule entities enable your team to model, track, and visualize small molecules in Benchling. Use them in the Registry to model chemical compounds, then search for and visualize your molecules using our chemical structure-based search capabilities.

Molecule entities enable you to create and model chemical compounds captured as chemical entities. With molecule entities, you can:

• View calculated physicochemical properties
• Find molecules via similarity and substructure search
• Visualize chemical structures

At a high level, you can create molecules in the Registry by: 

• Bulk importing via API, .sdf, or .csv
• Registration tables using SMILES strings
• Drawing chemicals using the Marvin JS chemical sketcher

The ability to make molecule entities is an add-on to core Benchling capabilities. To enable molecule entities for your organization, contact your CX representative and account manager. 

Create individual molecules by drawing the structure

You can create individual molecules in the global, project, or Registry create menus. The instructions below are for the global create menu.

Tip: To input schema fields during molecule creation, we recommend using the Registry create menu rather than the Global Create menu

To create a molecule:

1. Click Local Create button in the Registry 

2. Hover over Molecule, then click New Molecule

3. In the Create Molecule modal, enter the molecule name and select the folder

   • If you’re using the global or project create menus and select a schema, you’ll complete the schema fields later

4. Enter the chemical structure of the molecule or draw the molecule, then click Create

You can enter the chemical structure of your molecules by drawing the structure in the Marvin canvas or uploading a chemical structure. Tip: To enhance your workflow, use Marvin JS keyboard shortcuts.

Create molecules by uploading

You can import molecules in bulk from a spreadsheet, raw text, or .sdf file. To upload a chemical structure:

1. Click Global Create in the Navigation Bar

2. Hover over Molecule, then click Import Molecule 

3. Select which folder the Molecule should be associated with and optionally select a schema

4. You can select the file format from the drop-down menu or choose to let Marvin auto recognize the file format

   • If you’re using spreadsheet or .sdf, select Choose file. Select the file, then click Open

   • If you’re using raw text, enter or paste the text into the window

5. Upload the file and click Next

6. Ensure the column mappings are correct, and click Next 

7. Resolve any errors, and then click Import 

Note: If you’re importing from a spreadsheet, you can rely on a column of data representing chemical structure in SMILES or .mol file format; both must be in text/string format.

Supported file formats for chemical structure imports

Benchling supports many common and proprietary file formats. You can use the table below as a general reference to determine if a file type is supported, however, we’re continuously expanding our list of supported formats, so we always recommend first trying to upload your file into the importer, as it might not yet be included in this reference.

Registration tables

You can create new molecules and register existing molecules through registration tables by specifying a SMILES string to represent the chemical structure. When inserting a registration table for a molecule entity, a required smiles field is automatically added to the table. You don't need a defined schema field for SMILES.

Create molecules through the API

There are a variety of endpoints available through Capillary which can:

• Bulk archive molecules

• Bulk unarchive molecules

• Bulk update molecules

• Create bulk and single molecules

• Get a molecule by API identifier

• List all molecules

To learn more about these endpoints, visit the Molecules API documentation.

View physicochemical properties

With molecule entities, you can edit your chemical structures and review their properties. You can also archive, add and remove tags, and review and restore previous versions of your molecules. 

You can view the following properties calculated by RDKit by opening the molecule and clicking the Physicochemical properties tab: 

• Atom counts
• Calculated octanol/water ratio (cLogP)
• Molecular weight (MW)
• Topological polar surface area (TPSA)

View visual representations of chemical structures

To view the visual representation of a chemical structure, open the molecule and click the Chemical Structure tab. In this tab, you can also view the chemical formula and canonicalized SMILES string. Clicking into the Expanded Chemical Structure icon in the upper left of the Chemical Structure tab will allow you to open a viewing window that allows you to zoom and pan  

Edit chemical structure of molecules

From the chemical structure tab, users are able to edit the chemical structure. To edit the chemical structure, the user can draw a new chemical structure through MarvinJS or import a new molecule

Note: salts do not display on chemical structures. 

View and restore previous versions

Molecules are versioned like other entities on Benchling, where a new version of a molecule is created when a user updates its chemical structure.

To view, rename, and restore previous versions of a molecule:

1. Open the molecule, then click the history icon in the right-side panel
2. Select the version you want to review. The version will display in the Chemical Structures tab in read-only mode
3. To clone, restore, or rename a version, click:
4. Clone from version to create a new file with this version
5. Reset to version to restore this version
6. Update version after entering a version name to rename the version

Rename, move, archive, and tag molecules

To move, archive, or rename a molecule:

1. Click the info icon in the right-side panel
2. In the pop-up window, click:
   • Update information after entering a new name or selecting a different folder
   • Archive to archive the molecule

To manage tags:

1. Click the info icon in the right-side panel
2. Click the Tags tab in the pop-up window
3. Enter a tag name and optional value, then click Add to create and add a tag to the molecule
4. Hover over a tag and click the X to remove a tag from the molecule

Molecule search 

Benchling's chemical awareness for molecule entities supports additional search capabilities for registered Molecule entities. You can draw or upload a chemical structure to facilitate one of two chemical search functions: 

• Substructure search: allows you to see all molecules in Benchling that contain full or partial matches to the specific chemical features queries
• Similarity search: allows you to see all molecules in Benchling based on similarity to the chemical structure used as an input. Results are returned ranked in order of similarity to the input chemical

To perform a molecule search: 

1. Open the Global search function from the Navigation bar 
2. Click the Type dropdown menu and select the Entity/Molecule option
3. Click the Chemical Search icon at the right of the search bar
4. Draw the chemical structure in the MarvinJS canvas or upload the structure by clicking the Import icon in the upper left corner of the canvas 
5. Specify the search type by clicking the Substructure or Similarity option

6. Click Search 

    

FAQ

Q: Can I create or import molecules with atom group notation?

A: No. Molecule entities don’t support atom group notation like ambiguous molecules containing R-groups, atom lists, atom NOT lists, any atoms, etc. 

Q: How large can my structures be? 

A: Molecule entities cannot be larger than 2,000 atoms.

Q: Can I store multicomponent structures?

A: No. Multicomponent chemical structures can’t currently be stored as molecules. If you try to create a molecule with multiple components, an error displays.

Q: Can I display salts on chemical structures?

A:  Salts are automatically stripped from the file during conversion. The largest fragment of the original molecule by atom count is kept as the parent molecule, and all other fragments are treated as salts.

Salts can be saved in schema and custom fields when detected upon bulk import. They’re parsed and stored as a list of SMILES strings saved as a text field value.

Q: Can I create a molecule entity for a molecule that uses repeat notation? 

A: Yes, repeat notation brackets and multipliers that are typically found in large polymer structures are supported.