The code is developed based on the HPS model proposed by Dignon et al. (DOI and has been modified. The code uses a hydropathy scale called M3 for each of the amino acids, which was developed by Tesei et al. in 2021 (DOI).
To run the code for 33 IDPS (listed in idp_bank.csv), please follow the following procedure:
- Run master_IDPs.py, and when prompted, specify the index of the IDP sequence to run. This will create a directory with the name of the IDP.
- cd to the directory and run master.py. This will generate folders with epsilon values ranging from [0.1, 0.18, 0.2, 0.22, 0.25, 0.3, 0.4] and submit the batch job using the Slurm script.
- Finally, to gather the Rg values for different IDPs, run collect_Rg_data.py. This will generate subplots with all the Rg values for different epsilons.
If you have any questions or difficulty running, please contact:
Swarnadeep Seth: Swarnadeep.Seth@ucf.edu and
Aniket Bhattacharya: Aniket.Bhattacharya@ucf.edu