Supplementary Data for SILCS-RNA paper

---

FragMaps

The directory contains the SILCS FragMaps for all 7 RNAs studied in the paper along with an SDF file with all the respective ligands.

To visualize the FragMaps

1. Download the repository

git clone https://github.com/mackerell-lab/silcs-rna_paper.git OR [Click Here]

2. Enter the directory for an RNA

cd FragMaps/fmn/

3. Unzip the compressed fragmaps

tar -xzf silcs_fragmaps_5kx9.tgz

4. Enter the directory

cd silcs_fragmaps_5kx9

5. Use VMD or PyMOL to visualize

vmd -e view_maps.vmd OR pymol view_maps.pml

---

GCMC - Grand Canonical Monte Carlo (GCMC) Code

The directory contains the executable for GCMC code used in the SILCS-RNA paper: gcmc_v1.4.10

• Should run in Unix/Linux environments.

Usage : gcmc_v1.4.10 <input_file> <output_file> {optional: -nt <number_of_threads> }

An example is provided with all inputs and outputs in the example.tgz file.