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Sequence Design Results for the sample input

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Target Topology:

F-RAG run time: 51 minutes 23 seconds

Total number of sequences generated: 2553


Out of the lowest scoring unique sequences, a total of 12 sequences were generated that fold onto the correct topology, as predicted by RNAfold [15] and NUPACK [16, 17, 18]. Note that the score, calculated for the 3D tree graph of the atomic models generated by F-RAG (using a knowledge-based potential), is used only to select sequences for screening with RNAfold and NUPACK and does not indicate folding onto the target topology.
There may be additional sequences produced that are duplicates or do not fold onto the target topology. All sequences and their models are available for download.




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The following files are available to download (format information available on File Formats page):

Download Plots
Download Correct Sequences File
Download 200 Lowest Scores File
Download All Model Scores File
Download Generated Atomic Model PDB Files
Download All 3D Tree Graph Files
Download All Model BPSEQ Files

The atomic models generated by F-RAG are not optimized for energy or geometry and may contain chain breaks. The sequences corresponding to the 2D structures and 3D atomic models generated by F-RAG are not guaranteed to fold onto the target RNA-like topology using other RNA 2D structure prediction programs. For best results, we recommend running F-RAG for multiple orientations and subgraph decompositions of the target RNA-like topology, selecting atomic models without chain breaks and lowest scores (lower scores are better). We highly recommend further screening the sequences of the lowest scoring unique models by at least two different 2D structure prediction programs (like with RNAFold and NUPACK done here[4]).


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