PDNPR 0.1.0

Tool to find allosteric route based on MD files

Protein Dynamic Network Pathway Runner (PDNPR)

PDNPR is a tool for visualizing protein dynamic network paths, combining libraries such as PyMOL, NetworkX and MDTraj to achieve trajectory extraction, network construction, path analysis and visualization from molecular dynamics.

Run PDNPR

1. Make sure that the PDNPR environment is activated, then run the 'pdNPR.py' script:

• use PDNPR GUI

from PDNPR import GUI

• use PDNPR package

from PDNPR.PDNPR import pdnpr
pdnpr(step, start_AA, end_AA, edge_cutoff, md_file, pdb_file)

2. Set parameters

• On the GUI screen, enter the following parameters:

  • Step: retrieves the frame stride.
  • Start Amino Acid: indicates the start amino acid number.
  • End Amino Acid: indicates the number of the end amino acid.
  • Edge Cutoff: specifies the threshold of the edge weight.
  • Select file
  • Click the run button to select the Molecular Dynamics trajectory file (XTC file) and Protein structure file (PDB file).

• Run the task

  • The output area displays progress and information.
  • The task consists of the following steps:
    • Extract frames
    • Generating network
    • Merge networks
    • Calculate the shortest path
    • Generate and save PyMOL images
  • View results
  • After completion of the task, the output area will display the information of the shortest path, save the image and pse file, and automatically open the generated image file.