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:

Getting started

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.

Related topics

Creating and importing molecules

Managing and editing molecules

Searching molecules and chemical compounds

What is the Registry?

Did this answer your question?