Searching molecules

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Search for molecules from global, Projects, or Registry searches using Benchling’s chemical search functionality. Draw or upload your structure, then search two ways:

  • Substructure search: draw or upload a substructure with the Marvin JS sketcher and view the molecules that contain the substructure.

  • Similarity search: draw or upload a molecule and get results based on their similarity to the input molecule. Similarity searches are completed using Tanimoto Coefficient. The desired similarity default is 0.8 and can be adjusted in the drop-down menu in the search window.

Search for molecules

To perform a molecule search:

  1. Click the lens icon in the left-side menu to open global search.

  2. Click the Type drop-down menu and select Entity / Molecule to refine the search.

  3. Click the molecule icon on the right side of the search bar.

  4. Complete the chemical structure of the molecule by:

    • Drawing a chemical structure in the Marvin canvas

    • Uploading a chemical structure to Marvin by clicking the Import icon in the top-left corner of the canvas.

  5. Click Substructure or Similarity based on the type of search you want to perform. You might need to scroll down in the window to view these options.

  6. Click Search.


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