DYN_INTERFACES

Scripts to analyze the contacts at PPI during MD simulations.

The scripts rely on the ccmap and pypstruct packages, so you will need to install them in a local envt:

conda create -n dyn_interfaces python=3.8

conda activate dyn_interfaces

pip install ccmap

pip install pypstruct

Perform the following steps in the indicated order.

extract contacts from MD snapshots

cd CONTACT_ANALYSIS

source main.sh

cd -

Assess conservation of contacts over time

cd CONSERVATION_INITIAL_CONTACTS

source main.sh

cd -

Perform Clustering based on interface contacts

cd CLUSTERING

source main.sh

NB : to go further, you need to decide the number of clusters and write it in a file with the following format:

PDB_ID NB_CLUSTER

And then:

source main2.sh

Pick cluster centroids

cd CENTROIDS

source main.sh

cd ../..

Analyse contacts in each cluster

cd CLUSTER_CONTACT_ANALYSIS

source main.sh

cd ..

TO DO :

Compute Interface properties

cd DELTA_ASA

source main.sh

cd GAP_INDEX

source main.sh