A coarse-grained model of disordered RNA for simulations of biomolecular condensates

This repository contains codes, raw data and parameter files that used to reproduce the results in "A coarse-grained model of disordered RNA for simulations of biomolecular condensates by Yasuda, I., von Bülow, S., Tesei, G., Yamamoto E., Yasuoka K. & Lindorff-Larsen, K. (2024)".

Layout

• calvados/ Codes and installation guide to run CALVADOS 2-RNA simulation as implemented in this work.
• analysis/ Scrtipts to run analysis
• all-atom/ All-atom structures of UCAAUC from [Bergonzo ,C., Grishaev, A., Bottaro, S., RNA, 28, 937–946 (2022)], and HCG_models from [Pietrek, L. M., Stelzl, L. S., Hummer, G., J. Chem. Theory Comput., 20, 2246–2260 (2024).]
• single-chain/ Input files into calvados for single chain simulations of polyR30
• flory_exponent/ Input files to run single chain simulations of polyR10-100
• 400-chain/ Input files into calvados for 400-chain simulations of polyR30
• FUSRGG3/ Input files into calvados for FUSRGG simulations of polyR40
• MED1/ Input files into calvados for MED1 simulations of polyR40
• viewer1.ipynb Jupyter Notebook to produce plots for the paper figures (Figure 2).
• viewer2.ipynb Jupyter Notebook to produce plots for the paper figures (Figures 3 and 4).
• data/ Files to generarte figures

Simulations can be run using prepare_full.py

python prepare_full.py
cd {name}/{temperature}/
python run.py