Predict protein structures (beta)

  • Updated

More about this feature

Given Benchling’s focus on providing novel technology to support cutting-edge science, we’re excited to offer limited, beta access to protein structure prediction using AlphaFold 2. This beta feature enables users to predict the structure of a given protein sequence and interact with that 3D structure directly in Benchling. Until now, the AlphaFold AI system has been largely inaccessible to scientists with limited computing resources. Benchling wants to test what’s possible when more scientists can access this technology and leverage it in their scientific workflows.

If you don’t have access to Benchling’s protein structure prediction feature, you can join the waitlist.

Predicting protein structures

If you’ve gained access to our beta feature, request a protein structure prediction by navigating to the 3D Structure tab of the AA Sequence and selecting Predict 3D structure. You can only request structures for AA Sequences to which you have WRITE access.

As part of the beta program, you will have a limited number of requests for structure predictions.


You will be able to see that your request has been submitted. The prediction will take some time to process, so we will send you an email notification when it completes.

To view and interact with the predicted structure, navigate to back to the 3D Structure tab. Structures are rendered in Mol* Viewer; see this Mol* documentation to learn more about interacting with the structure.

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. In that case, select Redo structure prediction to replace the existing structure with a new predicted structure. 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 your 3D structures.

Notes about the beta program

Beta programs allow us to test new ideas quickly and develop impactful technology in partnership with our users. Please note that some of the tools we offer in beta may not be released broadly, based on user feedback. Throughout this program, we’d love to hear from you directly; don’t hesitate to share your feedback with us at or via this form.

Was this article helpful?

Have more questions? Submit a request