A Simple Example: Protein Folding

For this series of tutorials, all the code will be in the examples directory in the repo. After installing, Apptainer and ribbon, use the code in /examples/example1 to follow along!

Let's say we want to fold a protein from an amino acid sequence. We'll use Chai-1, a high-accuracy, ligand aware protein folding method. This requires a gpu!

First, we create a Task object, which sets up our Chai-1 job:

import ribbon
my_folding_task = ribbon.Chai1(
        fasta_file = 'my_sequence.fasta',   # Input FASTA
        output_dir = './out'                # Where the outputs will be stored
)

Then, we run the Task:

my_folding_task.run()

This can be shortened to a single command:

import ribbon
ribbon.Chai1(
        fasta_file = 'my_sequence.fasta',   # Input FASTA
        output_dir = './out'                # Where the outputs will be stored
).run()