RNamotiFold paper data
Year: 2025
Type: article
Abstract: A zipped copy of RNAmotiFold repo as of 10.08.2026 and full results for both benchmarks rcsb pdb and Rfam. For RNAmotiFold installation read the provided README.For the RNA 3D Motif Atlas conforming benchmark the same results were used but the instances specified in no_seq.csv and no_structure.csv were left out. All information on the benchmark and their evaluation is provided in the Materials & Methods section of the paper. The file rin_motif_mapping.json contains the mapping of RINs for RNAMoIP to RNA 3D Motifs. File Guide (RCSB Benchmark):input.fa: Fasta file with 3D structure sequences in Fasta formatinstances.txt: Individual Motif Instances with the Motif ID, Common Name, and Location as specified by the RNA 3D Motif Atlas. Beware locations my sometimes be off due to inconsitent numbering in the RCSB source data. Manual inspection of Loop/Structure/Sequence is sometimes required.Results Folder: Results of RNAmotiFold prediction for sequence with the same nameRNAmotiCes_Results Folder: Results for RNAmotiCes predictions for all Loops that were missed by RNAmotiFold File Guide (Rfam Benchmark):motif_matches.txt - All RMfam motif annotations in CSV format full_benchmark_set: CSV File with motif instances from motif_matches.txt file filtered to only contain motifs for the benchmark with e-value < 0.005no_seq: CSV File with the motif instances recognized to have no RNA 3D Motif Atlas conforming sequence in its motif annotated regionno_structure: CSV File with the motif instances recognized to have a RNA 3D Motif Atlas conforming sequence but no surrounding base pair can be formedBayesPairing2 Folder: Benchmark Results for full benchmark set from BayesPairing2, runtime has been added to JSON structure.Cacofold Folder: Benchmark results for full benchmark set from Cacofold-R3D, separated between Results subfolder for full outputs and Times subfolder for execution statistics.RNAMoIP Folder: Benchmark results for full benchmark set from RNAMoIP, seeparated between Results subfolder for full outputs and Times subfolder for exection statistics. Also includes mappign from Interaction networks to RNA 3D Motif Atlas structures.RNAmotiCes: Benchmark results for full benchmark set from RNAmotiCes, set up to identify all RNA 3D Motifs in every sequence. Separated into result CSV and log outputsRNAmotiFold: Benchmark results for full benchmark set from RNAmotiFold, set up to identify the lowest free energy structure for each motif in each sequence. Separated into results CSV and log outputs including runtime statistics.
Source: Figshare
Authors: Marius Sebeke, Björn Voß
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W6977158770
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