OpenKnotAI: code for RNA library design, SHAPE data processing, OpenKnot scoring, and RNA design methods
Year: 2026
Type: software
Abstract: 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.
Authors: Townley, Jill, Kladwang, Wipapat, Baker, David, Blair, Hamish M., Choe, Christian A., El Nesr, Gina, Favor, Andrew, Fisker, Eli, Haack, Daniel B., He, Shujun, Hingey, Jason, Huang, Po-Ssu, Huang, Rui, Joshi, Chaitanya K., Karagianes, Thomas G., Kubaney, Andrew, Liò, Pietro, Mancino, Adamo, Romano, Jonathan, Rudolfs, Boris, Spellmon, Nicholas, Toor, Navtej, Verma, Jigyasa, Wu, Vivian, Yu, Zhiheng, Eterna Participants, Das, Rhiju
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7164317865