CASP15_knotted_artifacts

Programs used in an article:
"Knotted artifacts in predicted 3D RNA structures"
Bartosz A. Gren, Maciej Antczak, Tomasz Zok, Joanna I. Sulkowska, Marta Szachniuk
PLOS Computational Biology, 2024

Required packages: topoly, tqdm
pip install -r requirements.txt to install them.

Project structure

pdb_models/ -- .pdb files of analysed CASP15 predicted models.
pdb_targets/ -- .pdb files of CASP15 targets.
pipeline_knots/ -- programs used to study knots in RNA.
pipeline_lassos_interlaces/ -- programs used to study lassos and interlaces in RNA.
secondary_structure/ -- script and input files to generate pictures of secondary structures of models from figures 5 and 6.
requirements.txt -- required packages.

Content of pipeline_knots/

1_pdb_to_xyz.py -- program which extracts RNA backbones from .pdb files and saves them as .xyz files. It outputs to xyz_models/ and xyz_targets.
2_check_topols.py -- main program for determining knot type of .xyz extracted RNAs. It outputs to res_models.txt and res_targets.txt.
3_vmd_cyclethrough.py-- program for manual checking of .pdb models listed in knots_to_verify.txt.
knots_to_verify.txt -- list of RNAs with knots after probabilistic closure or TTCs.

Content of pipeline_lassos_interlaces/

Pre-processing of 3D models:
clean-casp-headers.awk -- remove CASP-specific headers.

Identification and classification of entanglements of structural elements of 3D RNA models:
R*/*_report.csv -- entanglement identification and classification results obtained using RNAspider.
casp15-entanglements-summary.xlsx -- a comprehensive analysis of entanglements identified.

Lasso depth analysis:
1_normalize_csv.py -- a script normalizing CSV files.
2_analyze_depth.py -- a script preparing lasso depth analysis summary.
lasso-depth-analysis.xlsx -- the resultant summary.