Non-covalent Lasso Entanglement in IDPs

This repository contains code and data related to the study of non-covalent lasso entanglement (NCLE) in intrinsically disordered proteins (IDPs). The repository is organized into the following sections:

Protein Ensemble Database (PED) Statistics

• Analysis scripts and data for protein ensemble database statistics.
• Notebooks:
  • Compile_fig1.ipynb: Compiles Figure 1.
  • Fig. 1_Count_number_of_entries.ipynb: Counts the number of entries.
• Data files:
  • fully_idp.pkl, fully_structure.pkl, long_idr.pkl: Pickle files containing processed data.
  • PED_all_exp_entries.xlsx: Excel file with all experimental entries.
  • PED2023/: Code to retrive the disorder information from MobiDB and results of entanglement analyses of PED ensembles.

Coarse-Grain Simulation of Synthetic Polymer Chains

• Scripts and data for simulating synthetic polymer chains with different residue lengths (N=100, 200, 300).
• Scripts:
  • generate_synthetic_sequences.py: Generates synthetic sequences for simulation.
• Data files:
  • N100_results.pkl, N200_results.pkl, N300_results.pkl: Pickle files containing simulation results.
• Notebooks:
  • Plot_CG_simulations_superimpose_Phase_diagram_V2.ipynb: Plots and superimposes phase diagrams of the simulations.

Analysis of Human IDRs

• Analysis scripts and data for studying entanglement and functional enrichment in human intrinsically disordered regions (IDRs).
• Subdirectories:
  • Entanglement/: Contains scripts and data related to entanglement analysis.
  • GO/: Contains scripts and data related to functional enrichment analysis.

Simulation Codes

• Code to perform CG simulations: cosmo

Entanglement Code

• Code for entanglement analysis: entanglement_analysis