ARTEM-KT

Applying ARTEM to RNA tertiary motif search using kink-turns as an example.

Reference

E.F. Baulin, D.R. Bohdan, D. Kowalski, M. Serwatka, J. Świerczyńska, Z. Żyra, J.M. Bujnicki, (2024) ARTEM: a method for RNA tertiary motif identification with backbone permutations, and its example application to kink-turn-like motifs. bioRxiv. DOI: 10.1101/2024.05.31.596898

Check out our other developments

Content

cif

Kink-turns and isosteric motifs in mmCIF format

figures

Source figure files

introns

The seven representative group II intron structures in mmCIF format

othermotifs

Data on the G4, GNRA-tetraloop, i-motif, and parallel-pairing motif

refmotifs

Two reference motifs - a Kt7 kink-turn and a k-junction, in mmCIF format

sto_logo

Source files on the ribosomal k-junction conservation analysis

files

• REPRODUCE.md - The steps to reproduce the results
• TableS2.xlsx - Supplementary Table S2, 26,564 kink-turn matches obtained with ARTEM
• TableS3.xlsx - Supplementary Table S3, source benchmarking data
• 1ffk_hits.tsv - 11,025 kink-turn matches obtained with ARTEM against module #1
• 3d2g_hits.tsv - 18,727 kink-turn matches obtained with ARTEM against module #2
• annotated_hits.tsv - 26,564 kink-turn hits obtained with ARTEM and annotated with urslib2, source file for Supplementary Table S1
• kt7_13res_template.pdb - 13-residue kink-turn template used for benchmarking
• nrlist_3.312_4.0A.csv - Representative set of RNA structures
• pdb_download.py - Python script that downloads RNA-containing PDB entries
• post-processing.ipynb - Post-processing Jupyter Notebook
• unique_hits.py - Python script for merging 1ffk_hits.tsv & 3d2g_hits.tsv
• unique_hits.tsv - 26,564 kink-turn hits obtained with ARTEM, input for urslib2 annotation