This repository contains files used in a paper "Explicit description of viral capsid subunit shapes by expanding dihedrons" by Toyooka et al.

• docking_axes_viper/ contains notebooks for aligning the subunit coordinates with the VIPER coordinate system (Z-axis is the 2-fold axis, 3-fold axis is on the X-axis, and 5-fold axis is on the Y-axis)

• docking_pairwise/ contains input scipts and analysis notebooks for pairwise docking simulations for subunits

  • 1stm_zdock_iter/run.sh is a batch script for conducting docking simulations with ZDOCK
  • 1stm_zdock_iter/run_each.sh is a script for a single docking simulation with a specified random seed. Called from run.sh
  • 1stm_zdock_iter/skrew_parameters.ipynb analyzes the result of docking simulations. Sort the results accoring to docking scores and find the skrew axis of each docking pose
  • 1stm_zdock_iter/visualize.ipynb plots the docking score and the screw axis parameters, and also calculates and plots RMSDs from the reference structure (whole-shell structure)
  • 1stm_zdock_iter/ref.pdb is a sympolic link to a refrence structure (whole-shell structure)
  • 2buk_zdock_iter/ PDB ID: 2BUK
  • 4v4m_zdock_iter/ PDB ID: 4V4M
  • 6s44_zdock_iter/ PDB ID: 6S44
  • 7odw_zdock_iter/ PDB ID: 6ODW
  • 3r0r_zdock_iter/ PDB ID: 3R0R
  • 5zju_zdock_iter/ PDB ID: 5ZJU
  • 1stm_zdock_iter/ PDB ID: 1STM
  • 1vb4_zdock_iter/ PDB ID: 1VB4
  • 1m1c_zdock_iter/ PDB ID: 1M1C
  • 6r7m_zdock_iter/ PDB ID: 6R7M
  • 2m99_zdock_iter/ PDB ID: 2M99