Pipeline to extract protein interfaces for all the available Interactome3d structures in a given organism. The project automatically runs the following steps:
- Downloads all the necessary files for a given organism
- Splits the interacting partners into individual pdbs
- Runs NACCESS to calculate the accessbilities for the individual proteins as well as for the protein complexes.
- Calculates the difference on relative accessibility from complexes and monomers to detect residues changing their accessibiliy.
The pipeline prints the following files on the results directory:
accessibilities.tab. Contains all the relative accesibilities for all the residues present on the pdbs.interfaces.tab. Contains all the interface residues for each chain in each complex.
The remaining columns in the files contain additional information regarding the residues or the reliability of the protein structure (i.e. Structure, Model or Domain-Domain Model).
It requires naccess.
To run the pipeline, these are the two necessary commands.
make prepare
make all
If you want to run everything from scratch, clean the whole project running:
make clean
##Other organisms
So far, the pipeline has not been adapted to run different organisms. By default, it runs yeast. You can select other organisms by adding ORGANISM=ecoli (if you fancy running it on E. coli) at the end of each make command that you invoke. Remember to make clean before running a new organism.
The list of current organisms includes:
- Arabidopsis thaliana (athaliana)
- Canorhabditis elegans (celegans)
- Drosophila melanogaster (fly)
- Escherichia coli (ecoli)
- Helicobacter pylori (hpylori)
- Homo sapiens (human)
- Mus musculus (mouse)
- Mycobacterium tuberculosis (mtuberculosis)
- Saccharomyces cerevisiae (yeast)
Upcoming:
- Bacillus subtilis (bsubtilis)
- Campylobacter jejuni (cjejuni)
- Mycoplasma pneumoniae (mpneumoniae)
- Rattus norvegicus (rat)
- Plasmodium falciparum (pfalciparum)
- Schizosaccharomyces pombe (spombe)
- Treponema pallidum (tpallidum)