Evolution of human-virus PPI interfaces

Building a human-virus structural interaction network (SIN), resolving protein-protein interaction (PPI) interfaces, mapping and categorizing interfaces, and computing the evolutionary rates of different PPI interfaces.

Associated paper (by Su, W.-C. & Xia, Y.): Virus targeting as a dominant driver of interfacial evolution in the structurally resolved human-virus protein-protein interaction network.

Getting started

1. Clone this repository.

git clone 'https://github.com/wanchunsu/HV_PPI_interface_evolution.git'

2. Navigate to the downloaded folder.

cd HV_PPI_interface_evolution

3. Install requirements listed in dependencies.txt.

Usage

1. Navigate to the scripts directory.

cd scripts

2. Follow the instructions in the instructions.bash script. Below are the main steps in this pipeline:
   1. Build a human-virus SIN and resolve interaction interfaces.
   2. Map interfacial residues back onto human target proteins and categorize them.
   3. Determine the evolutionary rates of different PPI interfaces.

Note: The working directory is scripts and all data and results are stored in the data directory.

Software

• Python 3.9.12
• BLAST 2.13.0 (see https://www.ncbi.nlm.nih.gov/books/NBK52640/ for installation guide)
• DSSP (mkdssp) (installed in the install_dssp.bash script)
• MAFFT v7.490 (installed in the construct_msas.bash script)
• PAML (installed in the get_binned_dnds.bash script)
• PAL2NAL v14 (installed in the calc_site_specific_dnds.bash script)
• HyPhy 2.5.40 (installed in the calc_site_specific_dnds.bash script)

Databases

• IntAct (https://www.ebi.ac.uk/intact/home)
• PDB (https://www.rcsb.org/)
• UniProt (https://www.uniprot.org/)
• Ensembl (https://useast.ensembl.org/index.html)
• RefSeq (https://www.ncbi.nlm.nih.gov/refseq/)
• TimeTree (http://timetree.org/)

Contact

Wan-Chun Su wan.su@mail.mcgill.ca