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.
This article explains:
To use molecule entities, your tenant must have Sightglass 3 enabled. As of March 16, 2022, Sightglass 3 has been enabled on all tenants except GxP and academic tenants, and select individual tenants. If you experience issues with using molecule entities, contact your Benchling representative.
Molecule entity capabilities
Molecule entities enable you to create and model chemical compounds captured as chemical entities. With molecule entities, you can:
Calculate physicochemical properties
Find molecules via similarity and substructure search
Visualize chemical structures
You can create molecules in the Registry by:
Bulk importing via API, or via .csv and Registration tables using SMILES strings
Drawing chemicals using a chemical sketching tool
Uploading files with common chemical file formats such as SMILES, .mol, and .sdf
You can use substructure and similarity searches to track molecules in the Registry.
Molecule entity limitations
At this time, molecule entities don’t support:
Ambiguous molecules containing R-groups
Chemical structures larger than 999 atoms
Molecules with large repeat structures, like polymers
Organometallic compounds and inorganic compounds
Enabling molecule entities
To enable molecule entities for your organization, contact your CX representative and account manager.