Dataset and code for article "Explicit description of viral capsid subunit shapes by unfolding dihedrons"

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

- [grasshopper/] contains a GH file used in the 3D CAD Rhinoceros/Grasshopper.- [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/df.jld2] data containing top docking scores and poses, and screw motion parameters  - [1stm_zdock_iter/rmsd.jld2] RMSD data of docking poses with regard to the experimental structure  - [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)  - [4v4m_zdock_iter/] PDB ID: 4V4M  - [6s44_zdock_iter/] PDB ID: 6S44  - [7odw_zdock_iter/] PDB ID: 7ODW  - [3r0r_zdock_iter/] PDB ID: 3R0R  - [5zju_zdock_iter/] PDB ID: 5ZJU  - [1vb4_zdock_iter/] PDB ID: 1VB4  - [1m1c_zdock_iter/] PDB ID: 1M1C  - [6r7m_zdock_iter/] PDB ID: 6R7M  - [2m99_zdock_iter/] PDB ID: 2M99