Conformational dynamics and stability analysis of SARS-CoV-2 Spike glycoprotein

Trajectories of SARS-CoV-2 Spike Protein from four specific variants (Delta, BA.1, XBB.1.5, and JN.1) are included in this repository. The trajectories were generated by unbiased atomistic molecular dynamics in AMBER for a time of 500 ns (5 replicates of 100 ns). The simulations were performed with structures available in the Protein Data Base: Delta PDB ID: 7W92, BA.1 PDB ID: 7XO5, XBB.1.5 PDB ID: 8VKM, and JN.1 PDB ID: 8Y5J. The trajectories have been stored every 50 ps.

SCRIPTS:

add_chain.py: script to fix the chains in the Spike protein trimmer.

contact_map: Script to calculate contact map of a protein (used with the jupyter notebook, http://pomalab.ippt.pan.pl/GoContactMap/).

contact_frequency.ipynb: jupyter notebook to calculate inter-chain native contacts frecuency.

distance_RBD.tcl: script to calculate distances between 2 RBDs (defined by center of mass of the domains).

distance_NTD.tcl: scrpt to calculate distances between 2 NTDs (defined by center of mass of the domains).

angle.tcl: script to calculate angle values from 2 defined vectors.

Gausian_fitting.py: script to fit and plot the data of distances or angles (CVs). 

calculate_chi2.py: script to calculate the chi2 of the fitting data.

filter_contacts_interaction.py: script to filter the contacts from the list and calculate the type of interaction (ionic, polar, nonpolar, nonspecific).

get_frames_4_contacts.py: script to get the frames that are within the margen of the distribution (defined by mu and sigma).

cat_pdbs.sh: script to concatenate pdbs.

CONTACT MAPS: These files contains all the contact maps from the complete trajestories.

WT_CM 

DELTA_CM

BA1.CM

XBB15_CM

JN1_CM