This repository contains the code for computing the MD simulation result in the paper "DNA polymerase actively displaces single-stranded DNA binding protein"
The following dependencies should be enough to run all codes in this repository.
python==3.10.12
numpy>=1.24.2
pandas==2.0.0
matplotlib>=3.8.0
seaborn>=0.13.1
scipy>=1.10.1
biopython=1.83
mdanalysis==2.7.0
mdtraj=1.9.7
jupyter=1.0.0
For the three code in clustering_analysis folder:
- The pick_out_basin_from_wham.py script identifies the specific frame index that locates inside the local energy basin.
- The pick_out_and_save_basin_structures.py exports the structure from based on the index file that generated by pick_out_basin_from_wham.py.
- The drawing_clustermap_and_pick_representative.py file calculates the cluster centers and draws the hierarchically-clustered heatmap and dendrogram.
For four code in result_analysis folder:
- The calculate_ca_atom_rg_mdanalysis.py calculates the rg value of all CA atoms in a specific chain or the whold protein.
- The calculate_q_value_pdb1_pdb2_var_length_multi_chain.py calculates the Qw value for two structures. The Qw value was used to measure the pairwise distance between two structures, with a detailed explanation provided in Jin, S. et al. Protein Structure Prediction in CASP13 Using AWSEM-Suite. J. Chem. Theory Comput. 16, 3977–3988 (2020).
- The wham_calculation.py is the main script to calculate the 1D and 2D free energy profile based on the umbrella sampling result (energy and collective variables).
- The wham_mono_sampling.py checks the distribution of collective variable and energy files.