Improved Predictions of Phase Behaviour of IDPs by Tuning the Interaction Range

This repository contains Python code, Jupyer Notebooks and simulation data for reproducing the work of the scientific paper Improved Predictions of Phase Behaviour of Intrinsically Disordered Proteins by Tuning the Interaction Range by G. Tesei and K. Lindorff-Larsen DOI: 10.12688/openreseurope.14967.2.

Layout

• analyses.ipynb: Jupyter Notebook to analyze all the simulation data and generate plots
• calc_conc.ipynb: Jupyter Notebook to calculate c_sat and c_con from direct-coexistence molecular simulations
• prior.ipynb: Jupyter Notebook to carry out the analysis of the hydrophobicity scales collected by Simm et al. (DOI: 10.1186/s40659-016-0092-5)
• optimization/: Data and Python code related to the optimization of the residue-specific ``stickiness'' parameters
• SC/: Data and Python code related to single-chain simulations of the CALVADOS model. Simulations are performed using HOOMD-blue v2.9.3 installed with the mphowardlab/azplugins
• MC/: Data and Python code related to multi-chain simulations of the CALVADOS model in slab geometry. Simulations are performed using openMM v7.5
• supplementary_figures.pdf: Figures S1–S7 referenced in the paper

Python code and Jupyter notebooks are also available on GitHub at github.com/KULL-Centre/papers/tree/main/2022/CG-cutoffs-Tesei-et-al
Further usage examples of the CALVADOS model are available at github.com/KULL-Centre/CALVADOS.

Usage

To open the Notebooks, install Miniconda and make sure all required packages are installed by issuing the following terminal commands

bash conda env create -f environment.yml
source activate calvados
jupyter-notebook