HPC: Run AlphaPulldown on the HPC

In this exercise, we want to run a protein-protein interaction screening using the streamlined pipeline of AlphaPulldown, on the UGent HPC. Given the multiple steps of the pipeline, you will need to wait for queuing and computation times between jobs.

You can either choose your own FASTA files with proteins you would want to test, or reproduce the example from the training presentation using TSLP.fasta and IL2R_receptors.fasta.

Follow the steps here to run the different steps. In the end, you should end up with a .csv file containing metrics for the interactions that surpass the confidence threshold, that looks similar to this output file.