RNA-FRETools/Steffen_NucleicAcidsResearch_2024: v1.0.1

This repository contains structural models of the proof-of-concept de novo modeling trial of a manganese(II) sensing riboswitch (PDB 6n2v). The modeling code can be found here. The resulting models are organized as follows:

• 1_scored_by_rosetta_energy/ contains the top 10 models scored by the Rosetta energy function from FARFAR2 (Watkins, Structure 2020) was well as donor and acceptor accessible-contact volumes (ACV). The predicted mean FRET values computed by FRETraj and the Rosetta energy scores are listed in top10_rosetta_energy_FRET_prediction.csv

Visualize the ACVs on the structural models by running the following Python script from the PyMOL command line

run top10_rosetta_energy.py

• 2_scored_by_FRET_RMSD/ contains models filtered by a FRET treshold >0.4 and a RMSD < 15 A. All models are superimposed and aligned to the crystal structure (PDB 6n2v). The best model (no. 21) has a RMSD of 8.6 A to the crystal structure. The calculated RMSDs and Rosetta energy scores are listed in models_scored_by_FRET_and_RMSD.csv

Visualize the overlay of the low RMSD models


run 2.1_lowest_RMSD_model_overlay.py

Compare the individual models to the crystal structure

run 2.2_lowest_RMSD_model_to_crystal.py