Predict protein structures with AlphaFold

  • Updated

This feature enables users to predict the structure of a given protein sequence and interact with that 3D structure directly. Until now, the AlphaFold AI system has been largely inaccessible to scientists with limited computing resources. Now, scientists can leverage AlphaFold in their scientific workflows within the Molecular Biology application.

Request a protein structure prediction

Request a protein structure prediction by 

  1. Navigating to the 3D Structure tab of the AA Sequence 
  2. Selecting Predict 3D structure

You can only request structures for AA Sequences to which you have WRITE access.


Benchling supports predictions of proteins up to 1500 residues. If your request exceeds 1500 residues, a caution banner will display.

Screenshot 2023-04-07 at 9.21.41 AM.png

After submitting your request, the prediction will be processed. Benchling will send you an email notification when it is completed with a link to the prediction in Benchling.

In the event that a prediction fails, the user will be notified by email as well.


Viewing and Interacting with a Prediction

To view and interact with the predicted structure, navigate back to the 3D Structure tab. Structures are rendered in Mol* Viewer; see this Mol* documentation to learn more about interacting with the structure. Benchling returns only the top ranked structure (“rank 0”) predicted by the model.

Predictions are returned with pLDDT scores, which convey the model’s confidence. Regions of the structure are color-coded according to the model confidence; Benchling displays the same scoring and coloring as the AlphaFold database.

Screenshot 2023-04-07 at 9.33.59 AM.png

If a user highlights a region of the AA sequence, they can see the corresponding region highlighted in lime green in the structure.

Screenshot 2023-04-07 at 9.34.23 AM.png

You can also select Download to download the PDB file or Share to generate a share link to your AA Sequence and its predicted structure.


Note that if you change the residues in your AA Sequence, your structure will be out of sync and a yellow banner will appear. To replace the existing structure with a new predicted structure, click the Redo structure prediction button. By redoing the prediction, you’ll lose the out of sync structure, so we recommend that you download the original structure if you’d like to compare between versions.

Screenshot 2023-04-07 at 9.40.04 AM.png

Screenshot 2023-04-07 at 9.42.16 AM.png



Each customer may enable the AlphaFold feature on one tenant. A Benchling tenant will be limited to 10 predictions per month. 


A single Academic user is limited to 5 predictions per year.

*Note that only verified academic users (users whose accounts are associated with institution email addresses and whose email addresses have been verified) will be able to access AlphaFold.

Screenshot 2023-04-07 at 9.17.12 AM.png

All users on a customer tenant where AlphaFold is enabled will have the ability to request AlphaFold predictions. On the 3D structure tab, users can see how many prediction requests they/their tenant have remaining.

Validated Cloud

Currently AlphaFold is not available for Benchling Validated Cloud.


Was this article helpful?

Have more questions? Submit a request