Identification of 3D motifs in Rfam with JAR3D
James Roll, Craig L Zirbel · 2026
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Description
James Roll and Craig Zirbel present a tool that spots known three-dimensional shapes inside RNA sequences, in this paper from twenty twenty-six. Many working RNAs never code for protein; their jobs depend on how they fold. Loops in the fold often reuse a small set of proven shapes, called motifs, such as kink turns and T-loops.
Their program, JAR3D, compares the letters of a loop against a library of known motif shapes and reports the best matches. For this work they extended it to loops where three or four strands meet. They ran it over more than four thousand families in the Rfam database and posted the results on a public web page. Test cases outside the training set came out right. Internal loops matched known shapes far more often than hairpin loops or junctions, a pattern that tells its own story about RNA design.
Catalog record
| CREATOR | James Roll, Craig L Zirbel |
|---|---|
| YEAR | 2026 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 71 KB |
| VERSION | 1.0 |
| LICENSE | CC BY 4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |