[3dem] End-to-end automation of repeat-target cryo-EM processing in CryoSPARC

[Ali Punjani]

Dear 3DEM,

We are pleased to announce that we have released a new *end-to-end
automated workflow in CryoSPARC for repeat-target structure determination*
<https://urldefense.com/v3/__https://cryosparc.com/automated-workflows__;!!Mih3wA!D6RS5xAt7ejWguVhv06bXwwjSUwbYV_YyuXQ4f0ewFGh2xZeJTMro1oNbrSukNQo3BUQkct35eEeLGgKNLdI0jM9$ >. Using the strategies and tools
described in the *preprint*
<https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2025.10.17.682689v1__;!!Mih3wA!D6RS5xAt7ejWguVhv06bXwwjSUwbYV_YyuXQ4f0ewFGh2xZeJTMro1oNbrSukNQo3BUQkct35eEeLGgKNHmmMoaH$ >, it is now
possible to use automation to obtain results that match or exceed those
from manual processing. We demonstrate automated processing on 21 GPCR
datasets from EMPIAR.

Highlights:

   - *The automation strategy we developed can be set up once for any
   specific target class (e.g., active state GPCRs with Nb35) and reused to
   process multiple datasets fully hands-off.* It makes use of minimal
   prior knowledge through a low-resolution (~15Å) reference map.
   - *We tested the strategy across 21 challenging active and inactive
   state GPCR datasets.* Despite the small particle size and presence of
   contaminants, empty micelles, broken, denatured and aggregated particles,
   the automated workflow yielded equal or better resolution and map quality
   in 17 of 21 cases. In 10 cases, the automated results enabled improved
   model building of the ligand, binding pocket, side chain positioning and/or
   extracellular loops.
   - *All required jobs and tools are already available in CryoSPARC
   v4.7.1+.* The workflow is powered by new methods including micrograph
   junk detection, denoising and reference based auto-selection of 2D classes
   and 3D volumes. Please refer to the *preprint
   <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2025.10.17.682689v1__;!!Mih3wA!D6RS5xAt7ejWguVhv06bXwwjSUwbYV_YyuXQ4f0ewFGh2xZeJTMro1oNbrSukNQo3BUQkct35eEeLGgKNHmmMoaH$ > *for more
   insights and details.
   - *We provide downloadable Workflow JSON files so that users can
   replicate, adapt and extend the workflow for their own targets.* Please
   see cryosparc.com/automated-workflows for instructions and Workflow JSON
   files that you can start to use right away.

Thank you to all contributors to the EMPIAR repository.

Read the preprint on bioRxiv:
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2025.10.17.682689v1__;!!Mih3wA!D6RS5xAt7ejWguVhv06bXwwjSUwbYV_YyuXQ4f0ewFGh2xZeJTMro1oNbrSukNQo3BUQkct35eEeLGgKNHmmMoaH$ 

Please reach out on the CryoSPARC Discussion Forum:
discuss.cryosparc.com/c/automated-workflows.


Thank you!

CryoSPARC Team
Structura Biotechnology Inc.
https://urldefense.com/v3/__https://cryosparc.com/__;!!Mih3wA!D6RS5xAt7ejWguVhv06bXwwjSUwbYV_YyuXQ4f0ewFGh2xZeJTMro1oNbrSukNQo3BUQkct35eEeLGgKNBiryc2R$ 
https://urldefense.com/v3/__https://structura.bio/__;!!Mih3wA!D6RS5xAt7ejWguVhv06bXwwjSUwbYV_YyuXQ4f0ewFGh2xZeJTMro1oNbrSukNQo3BUQkct35eEeLGgKNEOHMHSg$ 
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