Tutorials

In this section you will learn how to generate an interaction fingerprint for different scenarios, how to extract information from the fingerprint data, and how to visualize it.

You can get a very brief overview of how ProLIF is implemented in the Summary section of this documentation, with links to the different modules for a more in-depth explanation.

All the examples here showcase a transmembrane protein (GPCR family) in complex with a small molecule. For convenience, the different files used for this tutorial are included with the ProLIF installation, and you can access these through either:

• prolif.datafiles.TOP and prolif.datafiles.TRAJ for the topology (PDB file) and trajectory (XTC file) used in the molecular dynamics tutorials.

• prolif.datafiles.datapath, which points to the directory containing all the other tutorial files. This is a pathlib.Path object which offers a convenient way to navigate filesystems as shown in their basic use section.

Warning

Outside of the tutorials, remember to switch any reference to prolif.datafiles with the actual paths to your inputs.

Tip

At the top of each tutorial’s page you can find links to either download the notebook or run it in Google Colab. You can install the dependencies for the tutorials with the command:

pip install prolif[tutorials]

Molecular dynamics

There are two tutorial notebooks for MD simulations, depending on the type of components that are being analyzed:

• Ligand-protein MD

• Protein-protein MD

Docking

Follow this tutorial for docking of a ligand with a protein:

Docking

PDB file

This tutorial showcases how to use ProLIF from a PDB file:

PDB

Advanced usage

For more advanced usecases such as modifying interaction parameters, defining your own interactions, ignoring backbone interactions and such, you can have a look at this tutorial:

Advanced usage