OpenKnotAI: code for RNA library design, SHAPE data processing, OpenKnot scoring, and RNA design methods
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Townley, Jill1
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Kladwang, Wipapat2
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Baker, David3
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Blair, Hamish M.4
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Choe, Christian A.5
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El Nesr, Gina6
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Favor, Andrew7
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Fisker, Eli8
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Haack, Daniel B.9
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He, Shujun10
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Hingey, Jason11
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Huang, Po-Ssu12
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Huang, Rui13
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Joshi, Chaitanya K.14
- Karagianes, Thomas G.15
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Kubaney, Andrew7
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Liò, Pietro14
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Mancino, Adamo16
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Romano, Jonathan17
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Rudolfs, Boris18
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Spellmon, Nicholas16
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Toor, Navtej18
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Verma, Jigyasa19
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Wu, Vivian2
- Yu, Zhiheng16
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Eterna Participants8
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Das, Rhiju20
- 1. Eterna Massive Open Laboratory; Frameshifter, San Francisco, CA, USA
- 2. Howard Hughes Medical Institute, Stanford, CA, USA
- 3. Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA
- 4. Department of Mathematics, Stanford University, Stanford, CA, USA
- 5. Department of Bioengineering, Stanford University, Stanford, CA, USA
- 6. Biophysics Program, Stanford University, Stanford, CA, USA
- 7. Department of Biochemistry, University of Washington, Seattle, WA, USA
- 8. Eterna Massive Open Laboratory
- 9. Department of Chemistry and Biochemistry, UC San Diego; A-Form Solutions, Inc., San Diego, CA, USA
- 10. Texas A&M University
- 11. A-Form Solutions, Inc., San Diego, CA, USA
- 12. Biophysics Program and Department of Bioengineering, Stanford University, Stanford, CA, USA
- 13. Department of Biochemistry, Stanford University, Stanford, CA, USA
- 14. Department of Computer Science and Technology, University of Cambridge, UK
- 15. Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA; Eterna Massive Open Laboratory; Frameshifter, San Francisco, CA, USA
- 16. Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- 17. Howard Hughes Medical Institute, Stanford, CA, USA; Eterna Massive Open Laboratory; Frameshifter, San Francisco, CA, USA
- 18. Department of Chemistry and Biochemistry, UC San Diego
- 19. Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- 20. Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford, CA, USA
Description
Code accompanying the OpenKnotAI study, “De novo design of RNA pseudoknots with deep learning” (preprint: https://doi.org/10.64898/2026.05.21.726960). This deposit bundles source-only snapshots (Git history removed) of the software used for RNA library design, SHAPE chemical-mapping data processing, OpenKnot scoring, and the RNA sequence/structure design methods evaluated in the study.
Each tool is provided as an individual .zip file so it can be downloaded and browsed separately. See README.md and MANIFEST.md for upstream URLs, commit SHAs (all retrieved 2026-06-11), licenses, and the role of each tool. Every bundled tool retains its own upstream LICENSE file.
Rosetta is third-party proprietary software and is linked, not redistributed (see LINKED-TOOLS-rosetta.md). Bulk experimental data (SHAPE sequencing reads, cryo-EM maps, design data) are deposited separately and cross-linked from this record.
Files
3DRNA.zip
Files
(499.7 MB)
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Additional details
Related works
- Is supplement to
- 10.64898/2026.05.21.726960 (DOI)
- References
- 10.5281/zenodo.18666308 (DOI)
- 10.5281/zenodo.20101887 (DOI)