Running the script find_interface

find_interface is a script that using the output provided by Alphafold3, provides different plots and files useful for the identification of interacting interfaces

Installation

Packages required to run the find_interface script are listed in the conda environment file environment.yml or requirements.txt

Conda environment can be activated with the instruction:

conda env create -f environment.yml

conda activate AlphaBridge

How to run the script

1. Download and unzip the folder from the AlphaFold server.

To run the script from the find_interface working directory, use

python3 define_interfaces.py -i path-to-AlphaFold3-folder

DEMO EXAMPLE

python3 define_interfaces.py -i /data/AF3/fold_1a02

The output will be saved in the same folder provided as an input.

OUTPUT FILES

The following files will be saved inside the input folder:

1. Confidance-contact_plot.png
2. Binding_interfaces.csv
3. interface_df_per_token.csv
4. matrix_info.json

Confidance-contact_plot PNG image with The Confidence-Contact Integration (CCI) plot (name subject to change). A two-dimensional graph where each token is represented along both the x and y axes. The plot is bisected diagonally into two sections. The upper section presents data on the overall confidence in the local structure and the relative positions of two tokens. The lower section of the Confidence-Contact Integration (CCI) plot illustrates the closeness of pairwise contacts between two tokens in the predicted structure.

Binding_interfaces

CSV file where all interfaces are listed, along with the involved entities involved in the interaction

Interface_df_per_token

CSV file with per-token level information

matrix_info

Json file with all information used to run this script.