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An integrated, pipeline-based approach for cryo-EM structure determination and atomic model refinement in the cloud

View ORCID ProfileMichael A. Cianfrocco, Indrajit Lahiri, Frank DiMaio, Andres E. Leschziner
doi: https://doi.org/10.1101/246587
Michael A. Cianfrocco
1Department of Cellular & Molecular Medicine, University of California – San Diego, La Jolla, CA, United States
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  • For correspondence: mcianfro@umich.edu
Indrajit Lahiri
1Department of Cellular & Molecular Medicine, University of California – San Diego, La Jolla, CA, United States
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Frank DiMaio
3Department of Biochemistry, University of Washington, Seattle, United States; Institute for Protein Design, University of Washington, Seattle, WA, United States
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Andres E. Leschziner
1Department of Cellular & Molecular Medicine, University of California – San Diego, La Jolla, CA, United States
2Section of Molecular Biology, Division of Biology, University of California – San Diego, La Jolla, CA, United States
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ABSTRACT

Access to streamlined computational resources remains a significant bottleneck for new users of cryo-electron microscopy (cryo-EM). To address this, we have built upon our previous work (Cianfrocco & Leschziner 2015) to develop software tools that will submit cryo-EM analysis routines and atomic model building jobs directly to Amazon Web Services (AWS) from a local computer or laptop. These new software tools (“cryoem-cloud-tools”) have incorporated optimal data movement, security, and cost-saving strategies, giving novice users access to complex cryo-EM data processing pipelines. Integrating these tools into the RELION processing pipeline and graphical user interface we determined a 2.2 Å structure of ß-galactosidase in ~55 hours on AWS. We implemented a similar strategy to submit Rosetta atomic model building and refinement to AWS. These software tools dramatically reduce the barrier for entry of new users to cloud computing for cryo-EM and are freely available at cryoem-tools.cloud.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 11, 2018.
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An integrated, pipeline-based approach for cryo-EM structure determination and atomic model refinement in the cloud
Michael A. Cianfrocco, Indrajit Lahiri, Frank DiMaio, Andres E. Leschziner
bioRxiv 246587; doi: https://doi.org/10.1101/246587
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An integrated, pipeline-based approach for cryo-EM structure determination and atomic model refinement in the cloud
Michael A. Cianfrocco, Indrajit Lahiri, Frank DiMaio, Andres E. Leschziner
bioRxiv 246587; doi: https://doi.org/10.1101/246587

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